[English] 日本語
Yorodumi
- PDB-4p00: Bacterial Cellulose Synthase in complex with cyclic-di-GMP and UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p00
TitleBacterial Cellulose Synthase in complex with cyclic-di-GMP and UDP
Components
  • (Cellulose Synthase ...) x 2
  • unidentified peptide
KeywordsTRANSFERASE / membrane protein / cellulose biosynthesis / biofilm / cyclic-di-GMP
Function / homology
Function and homology information


cellulose synthase (UDP-forming) / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / UDP-glucose metabolic process / cyclic-di-GMP binding / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4520 / Chitobiase; domain 2 - #20 / Chitobiase; domain 2 - #30 / : / Cellulose Synthase Subunit B, alpha-beta domain / Cellulose synthase, subunit A / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / Cellulose synthase / Glycosyltransferase like family 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4520 / Chitobiase; domain 2 - #20 / Chitobiase; domain 2 - #30 / : / Cellulose Synthase Subunit B, alpha-beta domain / Cellulose synthase, subunit A / Cellulose synthase BcsB, bacterial / Bacterial cellulose synthase subunit / Cellulose synthase / Glycosyltransferase like family 2 / predicted glycosyltransferase like domains / PilZ domain / PilZ domain / Chitobiase; domain 2 / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Galactose-binding domain-like / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Thrombin, subunit H / Jelly Rolls / Alpha-Beta Complex / Up-down Bundle / Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-C2E / DIUNDECYL PHOSPHATIDYL CHOLINE / URIDINE-5'-DIPHOSPHATE / Cellulose synthase catalytic subunit [UDP-forming] / Cyclic di-GMP-binding protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMorgan, J.L.W. / McNamara, J.T. / Zimmer, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM101001 United States
National Science Foundation (NSF, United States)DGE-1315231 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP.
Authors: Morgan, J.L. / McNamara, J.T. / Zimmer, J.
History
DepositionFeb 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Dec 24, 2014Group: Database references
Revision 2.0Sep 27, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _entity.formula_weight ..._atom_site.label_asym_id / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 2.1Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 2.2Nov 27, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cellulose Synthase A subunit
B: Cellulose Synthase B subunit
D: unidentified peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,39010
Polymers167,4363
Non-polymers5,9557
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15650 Å2
ΔGint-14 kcal/mol
Surface area56830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.490, 216.790, 219.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Cellulose Synthase ... , 2 types, 2 molecules AB

#1: Protein Cellulose Synthase A subunit


Mass: 90014.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: RSP_0333 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3J125, cellulose synthase (UDP-forming)
#2: Protein Cellulose Synthase B subunit


Mass: 76636.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: RSP_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3J126

-
Protein/peptide / Sugars , 2 types, 2 molecules D

#3: Protein/peptide unidentified peptide


Mass: 783.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Production host: Escherichia coli (E. coli)
#4: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2774.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,17,16/[a2122h-1b_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g4-h1_h4-i1_i4-j1_j4-k1_k4-l1_l4-m1_m4-n1_n4-o1_o4-p1_p4-q1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}}}}}}}}}}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 6 molecules

#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#9: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.38 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop
Details: 1.65-1.9 M Sodium Acetate, 100 mM Sodium Citrate (pH 3-3.5)
PH range: 3-3.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2013
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.2→49.62 Å / Num. obs: 53311 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.7
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.085 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.98 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 2714 5.1 %
Rwork0.208 --
obs0.21 53242 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 0 363 0 11029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211365
X-RAY DIFFRACTIONf_angle_d0.67315562
X-RAY DIFFRACTIONf_dihedral_angle_d13.8124281
X-RAY DIFFRACTIONf_chiral_restr0.0251818
X-RAY DIFFRACTIONf_plane_restr0.0031974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.25820.3221480.29822608X-RAY DIFFRACTION99
3.2582-3.32090.32191360.28382654X-RAY DIFFRACTION99
3.3209-3.38860.3191400.27442681X-RAY DIFFRACTION99
3.3886-3.46230.28261540.26572594X-RAY DIFFRACTION99
3.4623-3.54280.30351470.25592685X-RAY DIFFRACTION99
3.5428-3.63140.29771330.23942641X-RAY DIFFRACTION99
3.6314-3.72950.28411210.2212662X-RAY DIFFRACTION99
3.7295-3.83920.23561320.22252629X-RAY DIFFRACTION99
3.8392-3.96310.26961590.20912678X-RAY DIFFRACTION99
3.9631-4.10470.25171420.20232628X-RAY DIFFRACTION99
4.1047-4.26890.22331420.19352664X-RAY DIFFRACTION98
4.2689-4.46310.22241470.18472634X-RAY DIFFRACTION98
4.4631-4.69820.21391400.17432641X-RAY DIFFRACTION98
4.6982-4.99230.19761390.1722666X-RAY DIFFRACTION98
4.9923-5.37730.23531590.18422639X-RAY DIFFRACTION98
5.3773-5.91760.22341540.20242662X-RAY DIFFRACTION97
5.9176-6.7720.21011520.19752692X-RAY DIFFRACTION97
6.772-8.52470.19921250.18052709X-RAY DIFFRACTION97
8.5247-48.98570.19611440.20432761X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67820.745-0.1244.50220.70.42670.3554-0.16-0.03730.9439-0.2201-0.76280.1674-0.17220.52870.8229-0.5101-0.14090.84610.30860.8817-10.491121.3398-34.3259
20.52130.4752-0.44390.6233-0.14241.41560.0240.01270.21550.4969-0.1459-0.0366-0.53810.10070.09440.5385-0.0696-0.03370.56430.24060.5536-23.491812.5555-43.3231
33.37-1.58881.97043.9427-2.89626.72350.11270.35510.3419-0.1923-0.20360.07070.33770.95680.12510.8483-0.2219-0.02030.86280.24750.754-10.6147-2.3122-18.1214
42.18370.36790.18823.2187-0.77092.34390.0495-0.38430.03461.10850.09810.3467-0.7683-0.2927-0.11441.1454-0.05020.08130.66170.14990.5391-30.3569-11.3334-1.8417
52.40980.94661.62271.6613-1.595.5085-0.06970.3597-0.07810.26480.28980.42330.52430.0898-0.18710.6476-0.0413-0.04340.65120.09450.5631-32.1528-15.3619-30.2775
60.4478-0.22520.3321.4598-1.24182.32860.0307-0.1070.03890.83860.17770.0928-0.6057-0.1473-0.22630.851-0.07060.00280.56650.16410.6142-29.5373.1691-25.5885
71.6380.95151.94330.55591.05093.6495-0.4018-0.72880.34790.1203-0.71960.4013-0.4534-1.21070.13820.99880.32970.28320.86820.2090.7517-45.76118.7289-18.1523
82.60280.99693.06861.99512.02796.43780.4548-0.2445-0.02790.53440.53411.0650.6695-0.9997-0.59870.5741-0.08910.0370.84280.32450.7151-46.9604-14.2713-23.9435
90.3967-0.4860.12651.499-0.44380.8740.06830.28930.1832-0.03680.58930.40350.1051-0.9986-0.46430.3826-0.077-0.08030.73650.38370.7242-43.9828-0.6922-48.6792
101.6007-0.235-0.76192.649-0.57931.5218-0.11430.30820.0740.09720.07030.12160.2448-0.00680.05970.6305-0.1306-0.04640.49050.10490.5083-28.9662-39.5581-17.3907
111.80051.5219-1.63073.0322-2.6163.1465-0.20580.2197-0.41740.3186-0.2191-0.5999-0.21960.0440.18030.6897-0.0352-0.09790.62620.12250.5316-23.0665-23.2804-16.6535
123.58611.6317-0.87532.35310.02081.6648-0.3490.6993-0.6807-0.34950.34680.52520.7512-0.4172-0.0430.7161-0.2277-0.13390.85930.3180.7485-42.2386-15.4256-41.3623
132.32471.111-1.21522.1276-0.34025.6426-0.0703-0.4957-0.7641-0.01150.2058-0.25370.88120.648-0.06130.53490.0509-0.03070.56560.15790.5573-26.088737.9273-99.0972
141.95020.6904-0.48122.496-0.57882.1645-0.06120.26210.0097-0.4535-0.16530.15970.0796-0.33270.20080.50870.0485-0.0580.49120.0360.4893-38.081235.2537-99.5759
151.11332.3236-0.99235.4786-2.14631.04080.7022-1.0245-0.66731.0793-0.6489-0.58870.5113-0.3209-0.15290.9175-0.0652-0.11410.81590.20680.9719-43.937818.5767-93.6383
162.98250.94920.1251.4696-0.15271.9274-0.09510.18930.16180.01810.07260.0109-0.28110.2012-0.03370.62720.03390.00330.44850.07440.4173-18.468244.8848-100.2417
170.30340.7413-0.86542.353-2.75093.217-0.00751.4401-0.7288-0.79470.5546-0.0513-0.1294-0.2525-0.17930.9174-0.255-0.10771.0521-0.01090.8184-2.728147.9051-109.7356
183.1963-0.34580.72714.06370.78413.1669-0.07220.05240.8242-0.11340.159-0.5006-0.84090.3061-0.10310.7813-0.08250.10260.46080.00210.6623-11.759456.9315-102.9214
192.17170.69060.55821.784-0.09861.31950.1180.0223-0.03750.03160.00840.2847-0.2671-0.3033-0.09020.43260.10910.02910.60290.19990.5191-38.955827.5115-73.5723
200.60590.36320.43361.829-1.01422.20980.0853-0.23030.31830.1808-0.2125-0.2959-0.41580.34230.03720.4616-0.0816-0.02910.60660.16750.5745-9.382540.8192-80.6621
215.14281.44281.43945.12960.63035.2410.2176-0.3748-0.5961-0.1518-0.6088-1.28420.70710.28250.11210.49110.29930.04720.9410.31110.8536-0.435623.3539-85.7182
220.06630.03520.29982.0388-0.40461.5677-0.0265-0.5559-0.4996-0.4486-0.2376-0.47490.51380.79760.12270.54290.11770.0630.8830.37690.6843-18.135111.0772-67.8807
232.4655-1.0412-1.23292.6589-0.56742.5318-0.0243-0.0918-0.52-0.1304-0.2073-0.0329-0.21370.21230.20340.46160.0071-0.02640.52640.16750.5806-11.774128.4286-83.4912
240.9505-0.2246-0.34861.18510.80884.52090.4612-0.3223-0.05860.0239-0.396-0.2809-0.69110.5070.44160.4063-0.2808-0.1730.82470.30250.6015-11.029422.0222-47.304
259.5996-4.193-1.83957.0282-4.26795.3013-0.56290.4983-0.3626-0.4103-0.061-0.30410.42850.0923-0.01990.64210.0446-0.11690.5574-0.10761.29757.778119.6745-85.9036
262.3326-0.09850.1064.05531.63452.7703-0.17710.26550.3741-0.3731-0.1723-0.141-0.22290.264-0.23880.9236-0.35530.20380.62170.17421.09329.85630.8314-80.8676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:35)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 36:117)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 118:135)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 136:277)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 278:297)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 298:488)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 489:502)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 503:522)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 523:575)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 576:674)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 675:706)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 707:740)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 54:67)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 68:153)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 154:169)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 170:242)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 243:248)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 249:303)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 304:451)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 452:504)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 505:531)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 544:599)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 600:665)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 666:720)
25X-RAY DIFFRACTION25(CHAIN D AND RESID 169:174)
26X-RAY DIFFRACTION26(CHAIN D AND RESID 175:177)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more