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- PDB-2xtq: Structure of the P107A Colicin M mutant from E. coli -

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Basic information

Entry
Database: PDB / ID: 2xtq
TitleStructure of the P107A Colicin M mutant from E. coli
ComponentsCOLICIN-M
KeywordsANTIMICROBIAL PROTEIN / BACTERICIN
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium
Similarity search - Function
de novo design (two linked rop proteins) - #280 / Colicin M, catalytic domain / Colicin M / Colicin M / de novo design (two linked rop proteins) / Beta-Lactamase / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsHelbig, S. / Patzer, S.I. / Braun, V. / Zeth, K.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Activation of Colicin M by the Fkpa Prolyl Cis- Trans Isomerase/Chaperone.
Authors: Helbig, S. / Patzer, S.I. / Schiene-Fischer, C. / Zeth, K. / Braun, V.
History
DepositionOct 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_conn
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLICIN-M
B: COLICIN-M
C: COLICIN-M
D: COLICIN-M
E: COLICIN-M
F: COLICIN-M
G: COLICIN-M
H: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)235,8928
Polymers235,8928
Non-polymers00
Water8,125451
1
A: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: COLICIN-M


Theoretical massNumber of molelcules
Total (without water)29,4861
Polymers29,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.852, 63.114, 189.340
Angle α, β, γ (deg.)87.59, 82.17, 65.65
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 2 - 268 / Label seq-ID: 2 - 268

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
COLICIN-M


Mass: 29486.479 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05820
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 107 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN C, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN D, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN E, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN F, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN G, PRO 107 TO ALA ENGINEERED RESIDUE IN CHAIN H, PRO 107 TO ALA

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 48.09 % / Description: NONE
Crystal growpH: 6.5 / Details: 20% PEG3350 0.2 M NANO3, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→49 Å / Num. obs: 85754 / % possible obs: 89.5 % / Observed criterion σ(I): 1.7 / Redundancy: 1.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.4
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.5 / % possible all: 72.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XMX
Resolution: 2.31→48.68 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.843 / SU B: 21.383 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.553 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27261 4514 5 %RANDOM
Rwork0.24023 ---
obs0.24185 85754 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20.17 Å2-0.11 Å2
2---0.5 Å20.01 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.31→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16536 0 0 451 16987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216950
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9523051
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02152163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58624.267689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.932152704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4661557
X-RAY DIFFRACTIONr_chiral_restr0.0990.22596
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112799
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7841.510722
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.584217316
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.78536228
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8454.55729
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1065tight positional0.070.05
2B1065tight positional0.060.05
3C1065tight positional0.060.05
4D1065tight positional0.060.05
5E1065tight positional0.070.05
6F1065tight positional0.070.05
7G1065tight positional0.060.05
8H1065tight positional0.060.05
1A953loose positional0.075
2B953loose positional0.065
3C953loose positional0.065
4D953loose positional0.075
5E953loose positional0.075
6F953loose positional0.075
7G953loose positional0.075
8H953loose positional0.075
1A1065tight thermal0.150.5
2B1065tight thermal0.160.5
3C1065tight thermal0.140.5
4D1065tight thermal0.150.5
5E1065tight thermal0.150.5
6F1065tight thermal0.150.5
7G1065tight thermal0.150.5
8H1065tight thermal0.150.5
1A953loose thermal0.1610
2B953loose thermal0.1610
3C953loose thermal0.1510
4D953loose thermal0.1510
5E953loose thermal0.1510
6F953loose thermal0.1610
7G953loose thermal0.1510
8H953loose thermal0.1410
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 320 -
Rwork0.318 6081 -
obs--100 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.82750.22350.09810.3213-0.30210.8029-0.0034-0.04230.0561-0.01120.0043-0.07430.0069-0.0132-0.00090.05170.00710.01820.07880.0040.078712.432-3.072-7.645
20.3974-0.2057-0.38960.75130.55381.84660.00310.0360.09230.0091-0.0243-0.01520.0128-0.09130.02130.0672-0.01970.00840.0880.01350.0323-3.478-2.402-2.353
30.38390.1875-0.58790.8971-0.71981.41740.11770.00840.08540.125-0.0037-0.03-0.21-0.0494-0.11410.0807-0.02350.00430.0749-0.00360.04-8.8825.56510.17
40.4540.265-2.26991.3161-0.693312.0388-0.0003-0.01480.00410.1426-0.0534-0.04030.02570.1250.05370.03820.019-0.03450.0993-0.00310.0806-10.115-0.38610.878
53.40130.3572-0.42951.1928-0.98452.63780.07230.3159-0.1854-0.3392-0.0220.2540.07980.0644-0.05030.14110.0278-0.09340.0811-0.02870.0939-27.997-15.902-19.228
60.6772-0.17660.16350.488-0.10260.1520.0310.0114-0.1028-0.0871-0.03560.12040.01420.0450.00460.08380.0068-0.00420.12130.00480.0575-23.165-17.634-11.636
70.1061-0.37010.52741.3238-1.88832.70640.067-0.0205-0.0206-0.22010.04860.08210.2989-0.0894-0.11560.10710.04430.0210.14170.00850.0314-6.616-36.5091.861
80.6935-1.01220.72191.5082-1.15041.08240.00730.0221-0.05160.0073-0.01550.0524-0.0852-0.00610.00820.0693-0.00840.01140.07580.00370.0425-6.517-35.027-2.596
90.6755-0.9745-0.28361.46240.38780.2294-0.0237-0.00260.07250.10470.03-0.1397-0.044-0.1131-0.00620.12260.0196-0.04660.1780.00480.074812.481-4.325-35.986
100.3142-0.04640.19970.1117-0.08720.5521-0.00910.0095-0.0771-0.03120.0179-0.0510.0229-0.0601-0.00890.078-0.01010.00560.1010.01130.06715.672-2.25-46.549
110.493-0.22960.5460.748-0.80411.62730.05040.0531-0.1291-0.09850.0461-0.05290.1528-0.1117-0.09660.0934-0.02290.00070.0966-0.01490.0586-8.711-11.13-61.107
120.6698-0.0382.25470.60990.5968.55060.03170.03460.0283-0.09710.0045-0.120.03950.1713-0.03610.0814-0.03770.0360.1085-0.00420.0307-9.917-5.102-61.59
132.26310.35750.29881.1799-0.25870.20090.1974-0.26370.3660.0847-0.18090.20980.11230.0372-0.01650.1873-0.02390.02010.1367-0.07480.088924.710.337-31.573
140.52720.1782-0.01740.4751-0.00510.21030.0246-0.01070.06450.0374-0.05220.10080.02670.02440.02770.0799-0.01230.00450.11330.00180.03329.55412.156-39.078
150.3760.4075-0.88730.445-0.96622.10080.00110.02370.01710.01080.04410.0179-0.0114-0.0845-0.04510.0860.0029-0.03930.1570.01380.073645.97330.822-52.697
160.33980.6168-0.3161.1337-0.62090.5428-0.0098-0.00960.0411-0.0138-0.020.05030.0574-0.03540.02970.0726-0.0024-0.00280.09350.02080.062746.06229.536-48.069
171.0645-0.937-0.4910.84070.40630.5796-0.0165-0.0857-0.08070.0220.09950.08690.094-0.0533-0.08310.0572-0.0454-0.00360.11340.02440.0806-46.066-31.32458.02
180.4114-0.05570.21650.22-0.11650.3302-0.03190.04270.01750.04810.0653-0.0055-0.0069-0.0004-0.03330.05520.00510.01980.0938-0.00840.0593-46.512-33.91248.134
190.23060.0157-0.07520.352-0.020.86720.005-0.00930.1545-0.06020.04060.0374-0.02740.07-0.04570.05830.00170.00570.07550.00310.107-27.404-27.92937.912
200.52680.1456-2.46720.0634-0.673712.3278-0.010.04960.0085-0.0133-0.03460.02-0.3158-0.33210.04460.16240.0413-0.09550.09910.00010.1433-23.949-30.6132.133
211.1297-0.01020.87062.13151.44972.20480.2667-0.1309-0.0950.1456-0.0861-0.37250.0587-0.061-0.18060.2008-0.0821-0.09360.07920.05270.1446-5.631-46.05262.349
220.85540.1340.19710.64120.0350.59920.0265-0.0214-0.03160.0499-0.0462-0.06590.00790.00450.01970.08070.01010.00690.09290.00460.0106-10.63-47.954.814
230.07790.42540.2352.33881.2970.7239-0.00470.0117-0.0268-0.01340.0871-0.14510.00210.0633-0.08230.07690.00460.02140.09470.00740.0481-26.967-66.77141.243
241.07291.01180.7281.27091.05620.9399-0.0113-0.0133-0.1622-0.06730.037-0.075-0.10730.0487-0.02570.10330.009-0.00410.04180.00810.049-27.084-65.36245.759
251.3303-0.117-1.54890.22370.03471.89840.190.1320.2201-0.1391-0.031-0.2137-0.1007-0.0907-0.1590.18710.09810.11090.11520.05410.2598-31.956-77.44674.474
261.1495-0.2791-0.17070.28610.1160.34840.06950.02610.0452-0.02-0.0623-0.08490.0006-0.0306-0.00730.08050.01120.01070.0889-0.0050.0466-37.007-75.41382.046
270.00640.00720.01680.29610.70391.7021-0.02060.00090.00110.00050.0369-0.00010.00520.1395-0.01630.0630.0056-0.00060.093-0.0130.1162-53.557-56.35495.45
280.8185-0.9243-0.59821.23161.01071.0422-0.00090.04370.12920.0842-0.0159-0.0850.15870.010.01670.0746-0.00010.01030.05630.00390.057-53.594-58.04290.942
290.77510.7966-0.27790.8724-0.55682.03940.06920.05130.0010.07760.05620.0459-0.2335-0.0619-0.12540.07360.0515-0.03960.1239-0.01050.1073-72.368-91.86478.852
300.64340.02270.02420.0691-0.06650.11210.0292-0.0224-0.0630.01480.00110.04220.00660.0412-0.03020.09640.0050.00960.1167-0.01120.0537-66.288-89.66889.177
310.3652-0.1363-0.22290.38350.15550.49340.0363-0.1085-0.15130.1025-0.00010.0350.07940.0685-0.03620.1398-0.0081-0.01080.10470.03830.1311-51.197-98.785104.421
320.97130.49760.33570.3422-0.71629.97490.0537-0.0895-0.1410.0446-0.0626-0.08150.05960.26460.00890.09370.0672-0.00760.09040.0380.0612-50.128-92.729104.634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 105
2X-RAY DIFFRACTION2A106 - 164
3X-RAY DIFFRACTION3A165 - 253
4X-RAY DIFFRACTION4A254 - 271
5X-RAY DIFFRACTION5B2 - 30
6X-RAY DIFFRACTION6B31 - 145
7X-RAY DIFFRACTION7B146 - 164
8X-RAY DIFFRACTION8B165 - 271
9X-RAY DIFFRACTION9C2 - 29
10X-RAY DIFFRACTION10C30 - 163
11X-RAY DIFFRACTION11C164 - 253
12X-RAY DIFFRACTION12C254 - 271
13X-RAY DIFFRACTION13D2 - 30
14X-RAY DIFFRACTION14D31 - 145
15X-RAY DIFFRACTION15D146 - 164
16X-RAY DIFFRACTION16D165 - 271
17X-RAY DIFFRACTION17E2 - 29
18X-RAY DIFFRACTION18E30 - 105
19X-RAY DIFFRACTION19E106 - 253
20X-RAY DIFFRACTION20E254 - 271
21X-RAY DIFFRACTION21F2 - 30
22X-RAY DIFFRACTION22F31 - 145
23X-RAY DIFFRACTION23F146 - 164
24X-RAY DIFFRACTION24F165 - 271
25X-RAY DIFFRACTION25G2 - 30
26X-RAY DIFFRACTION26G31 - 145
27X-RAY DIFFRACTION27G146 - 164
28X-RAY DIFFRACTION28G165 - 271
29X-RAY DIFFRACTION29H2 - 29
30X-RAY DIFFRACTION30H30 - 161
31X-RAY DIFFRACTION31H162 - 253
32X-RAY DIFFRACTION32H254 - 271

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