[English] 日本語
Yorodumi
- PDB-3fof: Structural insight into the quinolone-DNA cleavage complex of typ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fof
TitleStructural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases
Components
  • (DNA topoisomerase 4 subunit ...Topoisomerase) x 2
  • DNA (5'-D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3')
  • DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3')
  • DNA (5'-D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3')
  • DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3')
KeywordsISOMERASE/DNA / quinolone / topoisomerase / DNA / protein-DNA cleavage complex / Streptococcus pneumoniae / moxifloxacin / Cell membrane / DNA-binding / Isomerase / Membrane / ATP-binding / Nucleotide-binding / ISOMERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal ...DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Gyrase A; domain 2 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MFX / DNA / DNA (> 10) / DNA topoisomerase 4 subunit A / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsLaponogov, I. / Sohi, M.K. / Veselkov, D.A. / Pan, X.-S. / Sawhney, R. / Thompson, A.W. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases
Authors: Laponogov, I. / Sohi, M.K. / Veselkov, D.A. / Pan, X.-S. / Sawhney, R. / Thompson, A.W. / McAuley, K.E. / Fisher, L.M. / Sanderson, M.R.
History
DepositionDec 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA topoisomerase 4 subunit A
B: DNA topoisomerase 4 subunit A
C: DNA topoisomerase 4 subunit B
D: DNA topoisomerase 4 subunit B
E: DNA (5'-D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3')
F: DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3')
G: DNA (5'-D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3')
H: DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3')
F: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
H: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,37110
Polymers194,5688
Non-polymers8032
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14040 Å2
ΔGint-119 kcal/mol
Surface area79350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.601, 121.601, 178.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 5:53 or resseq 56:165 or resseq...
21chain B and (resseq 5:53 or resseq 56:165 or resseq...
12chain C and (resseq 417:421 or resseq 423:443 or resseq...
22chain D and (resseq 417:421 or resseq 423:443 or resseq...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNLEULEUAA5 - 4795 - 479
21GLNGLNLEULEUBB5 - 4795 - 479
12THRTHRASNASNCC417 - 63638 - 257
22THRTHRASNASNDD417 - 63638 - 257

NCS ensembles :
ID
1
2

-
Components

-
DNA topoisomerase 4 subunit ... , 2 types, 4 molecules ABCD

#1: Protein DNA topoisomerase 4 subunit A / Topoisomerase / ParC55 / Topoisomerase IV subunit A


Mass: 56455.434 Da / Num. of mol.: 2 / Fragment: residues 1-488
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: parC, SP_0855 / Production host: Escherichia coli (E. coli) / References: UniProt: P72525, EC: 5.99.1.-
#2: Protein DNA topoisomerase 4 subunit B / Topoisomerase / ParE30 / Topoisomerase IV subunit B


Mass: 30415.703 Da / Num. of mol.: 2 / Fragment: residues 404-647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: parE, SP_0852 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59961, EC: 5.99.1.-

-
DNA chain , 4 types, 4 molecules EFGH

#3: DNA chain DNA (5'-D(P*AP*CP*CP*AP*AP*GP*GP*TP*CP*AP*TP*GP*AP*AP*T)-3')


Mass: 4602.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA / References: PDB-3FOE
#4: DNA chain DNA (5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3')


Mass: 5810.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA / References: PDB-3FOE
#5: DNA chain DNA (5'-D(P*CP*TP*GP*TP*TP*TP*TP*AP*CP*GP*TP*GP*CP*AP*T)-3')


Mass: 4565.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA / References: PDB-3FOE
#6: DNA chain DNA (5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3')


Mass: 5846.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: E-site DNA / References: PDB-3FOE

-
Non-polymers , 1 types, 2 molecules FH

#7: Chemical
ChemComp-MFX / 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid / moxifloxacin / Moxifloxacin


Mass: 401.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24FN3O4 / Comment: antibiotic*YM

-
Details

Sequence detailsFOR CHAIN A AND B, THE DATABASE REFERENCE SEQUENCE IS REFERRED IN REFERENCES 1 AND 4 OF PARC_STRPN, ...FOR CHAIN A AND B, THE DATABASE REFERENCE SEQUENCE IS REFERRED IN REFERENCES 1 AND 4 OF PARC_STRPN, UNIPROT. THE 257TH RESIDUE IS THR ACCORDING TO THEM. FOR CHAIN C AND D, THE DATABASE REFERENCE SEQUENCE IS REFERRED IN REFERENCES 1 AND 4 OF PARE_STRPN, UNIPROT. THE 460TH AND 644TH RESIDUES ARE ILE AND ALA, RESPECTIVELY, ACCORDING TO THEM.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM Na cacodylate, 100mM Ammonium acetate, 15mM Magnesium acetate, 7.5% isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na cacodylate11
2Ammonium acetate11
3Magnesium acetate11
4isopropanol11
5Na cacodylate12
6Ammonium acetate12
7Magnesium acetate12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.2→34.067 Å / Num. obs: 44580 / Biso Wilson estimate: 178.14 Å2

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2NOV and 2RGR

2nov

2rgr


Resolution: 4→34.066 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 2492 10.1 %random
Rwork0.239 22193 --
obs0.2441 24685 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 150.002 Å2 / ksol: 0.185 e/Å3
Displacement parametersBiso max: 638.86 Å2 / Biso mean: 198.798 Å2 / Biso min: 44.54 Å2
Baniso -1Baniso -2Baniso -3
1--7.561 Å20 Å2-0 Å2
2---7.561 Å20 Å2
3----11.421 Å2
Refinement stepCycle: LAST / Resolution: 4→34.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7020 1374 104 0 8498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088909
X-RAY DIFFRACTIONf_angle_d1.20812589
X-RAY DIFFRACTIONf_chiral_restr0.0511488
X-RAY DIFFRACTIONf_plane_restr0.0121471
X-RAY DIFFRACTIONf_dihedral_angle_d17.9182472
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2427X-RAY DIFFRACTIONPOSITIONAL
12B2427X-RAY DIFFRACTIONPOSITIONAL0.047
21C980X-RAY DIFFRACTIONPOSITIONAL
22D980X-RAY DIFFRACTIONPOSITIONAL0.061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.07690.31081490.26871279X-RAY DIFFRACTION100
4.0769-4.160.3141600.25091202X-RAY DIFFRACTION100
4.16-4.25030.30151330.23031264X-RAY DIFFRACTION100
4.2503-4.3490.26741510.22131235X-RAY DIFFRACTION100
4.349-4.45750.27871330.22051246X-RAY DIFFRACTION100
4.4575-4.57780.28211360.21081246X-RAY DIFFRACTION100
4.5778-4.71210.25941420.21321261X-RAY DIFFRACTION100
4.7121-4.86380.2341150.19761276X-RAY DIFFRACTION100
4.8638-5.03710.26171530.21721235X-RAY DIFFRACTION100
5.0371-5.23810.28931400.23461221X-RAY DIFFRACTION100
5.2381-5.47560.2981390.25081235X-RAY DIFFRACTION100
5.4756-5.7630.36131320.26991272X-RAY DIFFRACTION100
5.763-6.12210.37741520.2871225X-RAY DIFFRACTION100
6.1221-6.59160.31951510.28961239X-RAY DIFFRACTION100
6.5916-7.24920.31291310.24721260X-RAY DIFFRACTION100
7.2492-8.2850.23181270.21681233X-RAY DIFFRACTION100
8.285-10.38880.23511370.17821253X-RAY DIFFRACTION99
10.3888-34.06680.29861110.26321011X-RAY DIFFRACTION81
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)
10.80330.9231-1.34583.1989-0.84371.86360.022-0.0211-0.58280.3214-0.9026-0.49130.00150.35590.92880.5972-0.25930.83220.22350.96380.6875-15.610231.8828.4771
2-0.3350.11020.7114-0.04071.2406-2.3992-0.44790.28430.2572-0.26190.003-0.026-1.02471.46190.26140.1699-1.1675-0.29331.54280.07430.0321-21.688150.619830.8215
3-4.9397-1.51730.57752.554-1.42140.7405-0.50910.5922-0.26140.17950.76690.8655-0.1395-1.3321-0.35520.5780.87590.58592.11271.13411.1187-4.926443.3251-25.2525
4-8.0854-4.33652.0456.05881.62520.5729-0.8233-0.48620.08220.1201-0.85682.21310.04090.49791.70110.68090.22020.34450.98170.20451.59186.528856.057-31.3621
53.2395-1.1508-0.68751.22391.90492.7451-1.13880.7135-1.07190.2174-0.32051.18460.0101-0.05181.39670.3452-0.23350.27030.3674-0.06051.0421-25.987440.3513-15.8728
6-2.58880.4584-0.64590.7676-1.16764.63540.36480.07890.1680.0993-2.0814-1.3393-0.112.23721.67430.9142-0.02320.07382.26811.51141.2812-20.369128.570620.0143
78.44775.36383.95499.76463.96082.56661.2791-1.4191.0327-1.3694-0.3472-1.2282-0.4275-0.3452-0.88081.2415-0.26260.83621.2641-0.14061.6177-34.993616.5435-44.3997
80.49914.4890.42762.01966.39640.27050.219-0.0901-0.52761.63360.0210.25950.81860.0162-0.2661.7913-0.19830.60770.86530.30431.9433-23.69618.4326-5.075
90.604-1.1132-0.4112.147-0.99411.9452-0.54440.1487-0.61221.6113-0.54460.76740.47250.10781.11771.6231-0.06681.02420.51820.01920.7526-15.87518.6774-20.0404
10-0.13970.44670.37894.15490.53380.9942-0.2144-0.2505-0.0940.6569-0.45460.33310.1016-0.28180.43670.29310.0513-0.8214-0.5741-1.52420.3778-45.158173.41288.4778
110.51040.6183-1.71020.3209-1.804-0.0747-0.77690.6019-0.2604-0.46130.28190.05931.1395-1.61380.25630.4552-1.00950.32061.27580.1525-0.3208-39.151954.564930.521
120.0101-0.39410.55-0.2772-0.15240.3804-0.3127-0.54010.4955-0.0392-0.0762-0.0148-0.0148-0.18180.33120.38821.187-1.01381.8492-1.39031.2251-55.941361.7837-25.7459
131.1376-4.04671.28654.2143-0.40921.7037-1.2483-1.14260.7782-0.0941-0.4316-0.7156-0.1593-0.79011.63120.96410.269-0.32311.0698-0.34361.2757-67.329749.2469-31.351
140.78060.01320.11851.3339-1.54522.4366-0.96170.51690.53050.0829-0.3952-1.0750.0352-0.12421.18180.2612-0.2217-0.38840.38660.08451.0593-34.84164.9615-15.8228
15-0.96610.098-1.96542.81082.57420.55590.59340.1256-0.13310.4052-1.63030.80310.1128-1.66331.05170.8085-0.0463-0.0782.084-1.26060.8187-40.393776.729920.0119
16-3.1113-1.4970.58683.0086-1.482.56560.8817-0.6164-1.0364-0.2237-0.8113-0.854-0.20560.30350.03781.2156-0.3738-0.77981.51060.32332.167-25.569288.7202-44.7324
174.2743-0.9535-3.70693.88830.36142.99640.503-0.02130.06932.89430.057-0.9095-0.3058-0.1106-0.5792.0144-0.1522-0.25910.8377-0.44611.5002-37.09486.8614-5.0839
180.5822-0.98750.96433.4740.50040.514-0.37950.16340.63082.1059-0.6095-1.0919-0.9766-0.15231.04631.59310.0059-0.99860.4065-0.0220.7493-44.93986.586-19.7203
19-2.41231.16448.36514.1504-1.02392.9236-0.28060.84390.1161.06041.14730.264-0.67353.4775-0.79161.5555-0.1560.83072.2794-0.07491.1992-7.095965.6835-12.5935
20-0.02380.5461-0.33190.22120.31640.5845-0.26351.4143-0.3197-0.1280.30750.07820.0923-0.6845-0.05670.03830.34171.00712.02540.27710.28053.83139.51-36.0933
210.25120.23360.55780.6065-0.18040.42350.13620.8043-0.099-0.0508-0.03160.566-0.24680.77920.01130.383-0.17480.14061.58820.51510.6121-6.05759.0369-38.6769
226.56820.0201-1.1124-0.80230.7658-0.6489-0.15742.183-0.83330.09421.0078-0.22210.0070.918-0.80821.2851-0.3634-0.32571.9331-0.34491.4592-53.774939.6894-12.7049
237.30212.29336.3246-0.0131.56674.879-0.35412.8160.4651-0.05030.4066-0.20890.01313.1272-0.0068-0.33260.4339-1.02171.8945-0.18-0.0693-64.663265.8147-35.9947
24-0.4860.1034-0.21081.5016-0.03060.39690.09060.62620.1714-0.0213-0.0262-0.85820.223-0.6789-0.00090.3968-0.18370.03391.5491-0.49730.686-54.639945.7493-38.3653
251.29660.46341.5041-1.7797-0.54977.15670.38631.19350.5147-0.63660.30740.07992.6711.2203-0.57841.5753-0.62970.09921.62510.00290.5355-16.883833.4132-45.5821
263.00561.8862-0.2004-0.16080.21966.47370.37891.1098-0.6838-0.7368-0.0343-0.1952-2.3712-1.0876-0.31911.689-0.1893-0.0181.6263-0.16310.5203-43.865771.8259-45.6433
271.40360.91282.25140.07180.19150.5534-0.31450.14260.10240.0178-0.52570.35440.0027-1.15250.8331.5404-0.1442-0.62333.183-1.71914.1381-38.029655.5254-33.8058
28-3.5325-1.89493.69990.1301-0.29531.0518-0.17060.27530.01860.00480.35650.5232-0.01440.1997-0.18551.7909-0.3601-0.12293.93671.8772.8075-22.624849.8571-34.3225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 343:382
2X-RAY DIFFRACTION2chain A and resseq 383:429
3X-RAY DIFFRACTION3chain A and resseq 18:30
4X-RAY DIFFRACTION4chain A and resseq 5:17
5X-RAY DIFFRACTION5chain A and resseq 31:154
6X-RAY DIFFRACTION6chain A and resseq 430:455
7X-RAY DIFFRACTION7chain A and resseq 239:322
8X-RAY DIFFRACTION8chain A and resseq 456:479
9X-RAY DIFFRACTION9chain A and not (resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 5:17 or resseq 18:30 or resseq 456:479)
10X-RAY DIFFRACTION10chain B and resseq 343:382
11X-RAY DIFFRACTION11chain B and resseq 383:429
12X-RAY DIFFRACTION12chain B and resseq 18:30
13X-RAY DIFFRACTION13chain B and resseq 5:17
14X-RAY DIFFRACTION14chain B and resseq 31:154
15X-RAY DIFFRACTION15chain B and resseq 430:455
16X-RAY DIFFRACTION16chain B and resseq 239:322
17X-RAY DIFFRACTION17chain B and resseq 456:479
18X-RAY DIFFRACTION18chain B and not (resseq 343:382 or resseq 383:429 or resseq 31:154 or resseq 430:455 or resseq 239:322 or resseq 5:17 or resseq 18:30 or resseq 456:479)
19X-RAY DIFFRACTION19chain C and resseq 539:581
20X-RAY DIFFRACTION20chain C and resseq 610:634
21X-RAY DIFFRACTION21chain C and not (resseq 539:581 or resseq 610:634)
22X-RAY DIFFRACTION22chain D and resseq 539:581
23X-RAY DIFFRACTION23chain D and resseq 610:634
24X-RAY DIFFRACTION24chain D and not (resseq 539:581 or resseq 610:634)
25X-RAY DIFFRACTION25chain E or chain F
26X-RAY DIFFRACTION26chain G or chain H
27X-RAY DIFFRACTION27chain F and resid 0
28X-RAY DIFFRACTION28chain H and resid 0

+
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