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- PDB-2j58: The structure of Wza -

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Basic information

Entry
Database: PDB / ID: 2j58
TitleThe structure of Wza
ComponentsOUTER MEMBRANE LIPOPROTEIN WZA
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


polysaccharide transmembrane transporter activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / wza like fold / wza like domain / : / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Polysaccharide export protein / Outer-membrane lipoprotein Wza, C-terminal domain / Polysaccharide biosynthesis/export protein / Outer-membrane lipoprotein Wza C-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #70 / wza like fold / wza like domain / : / Outer membrane lipoprotein wza fold like / Outer membrane lipoprotein wza domain like / Polysaccharide export protein / Outer-membrane lipoprotein Wza, C-terminal domain / Polysaccharide biosynthesis/export protein / Outer-membrane lipoprotein Wza C-terminal domain / Soluble ligand binding domain / SLBB domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEXANE / N-OCTANE / Putative outer membrane lipoprotein Wza
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsDong, C. / Naismith, J.H.
CitationJournal: Nature / Year: 2006
Title: Wza the Translocon for E. Coli Capsular Polysaccharides Defines a New Class of Membrane Protein.
Authors: Dong, C. / Beis, K. / Nesper, J. / Brunkan-Lamontagne, A.L. / Clarke, B.R. / Whitfield, C. / Naismith, J.H.
History
DepositionSep 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OUTER MEMBRANE LIPOPROTEIN WZA
B: OUTER MEMBRANE LIPOPROTEIN WZA
C: OUTER MEMBRANE LIPOPROTEIN WZA
D: OUTER MEMBRANE LIPOPROTEIN WZA
E: OUTER MEMBRANE LIPOPROTEIN WZA
F: OUTER MEMBRANE LIPOPROTEIN WZA
G: OUTER MEMBRANE LIPOPROTEIN WZA
H: OUTER MEMBRANE LIPOPROTEIN WZA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,94740
Polymers320,8068
Non-polymers3,14032
Water29,4371634
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area84850 Å2
ΔGint-530.8 kcal/mol
Surface area103730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.719, 215.268, 220.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52E
62F
72G
82H
13A
23B
33C
43D
53E
63F
73G
83H
14A
24B
34C
44D
54E
64F
74G
84H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A89 - 169
2112B89 - 169
3112C89 - 169
4112D89 - 169
5112E89 - 169
6112F89 - 169
7112G89 - 169
8112H89 - 169
1122A172 - 249
2122B172 - 249
3122C172 - 249
4122D172 - 249
5122E172 - 249
6122F172 - 249
7122G172 - 249
8122H172 - 249
1132A256 - 342
2132B256 - 342
3132C256 - 342
4132D256 - 342
5132E256 - 342
6132F256 - 342
7132G256 - 342
8132H256 - 342
1142A346 - 373
2142B346 - 373
3142C346 - 373
4142D346 - 373
5142E346 - 373
6142F346 - 373
7142G346 - 373
8142H346 - 373

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
OUTER MEMBRANE LIPOPROTEIN WZA / WZA


Mass: 40100.812 Da / Num. of mol.: 8 / Fragment: MATURE PROTEIN, RESIDUES 21-379
Source method: isolated from a genetically manipulated source
Details: ACYLATED AT CYS 21 SELENOMETHIONINE DERIVATIVE. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: O9A\:K30 / Plasmid: PWQ126 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): LE392 / References: UniProt: Q9X4B7
#2: Chemical
ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18
#3: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1634 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MATURE PROTEIN IS CLEAVED AND ACYLATED AT RESIDUE 21 (CYS). THE PROTEIN IS ALSO CLEAVED IN THE ...THE MATURE PROTEIN IS CLEAVED AND ACYLATED AT RESIDUE 21 (CYS). THE PROTEIN IS ALSO CLEAVED IN THE EXPRESSION STRAIN.

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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: 3.39 Å3/Da / Density % sol: 63.41 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.26→108 Å / Num. obs: 200359 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.4
Reflection shellResolution: 2.26→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.8 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→107.83 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.911 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 10587 5 %RANDOM
Rwork0.188 ---
obs0.19 200359 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.25→107.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22040 0 192 1634 23866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02222584
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9730688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19452832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97524.918976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.887153808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.92315128
X-RAY DIFFRACTIONr_chiral_restr0.0850.23576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216808
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.310758
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.515411
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.53161
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.340
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.171.514406
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.165222992
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28239123
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2454.57696
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A324tight positional0.030.05
12B324tight positional0.030.05
13C324tight positional0.030.05
14D324tight positional0.030.05
15E324tight positional0.030.05
16F324tight positional0.030.05
17G324tight positional0.030.05
18H324tight positional0.040.05
21A312tight positional0.030.05
22B312tight positional0.030.05
23C312tight positional0.040.05
24D312tight positional0.030.05
25E312tight positional0.040.05
26F312tight positional0.040.05
27G312tight positional0.040.05
28H312tight positional0.040.05
31A348tight positional0.040.05
32B348tight positional0.040.05
33C348tight positional0.040.05
34D348tight positional0.050.05
35E348tight positional0.040.05
36F348tight positional0.040.05
37G348tight positional0.050.05
38H348tight positional0.040.05
41A112tight positional0.040.05
42B112tight positional0.030.05
43C112tight positional0.040.05
44D112tight positional0.030.05
45E112tight positional0.040.05
46F112tight positional0.040.05
47G112tight positional0.040.05
48H112tight positional0.040.05
11A304medium positional0.450.5
12B304medium positional0.420.5
13C304medium positional0.550.5
14D304medium positional0.430.5
15E304medium positional0.440.5
16F304medium positional0.470.5
17G304medium positional0.370.5
18H304medium positional0.450.5
21A279medium positional0.350.5
22B279medium positional0.450.5
23C279medium positional0.410.5
24D279medium positional0.360.5
25E279medium positional0.510.5
26F279medium positional0.480.5
27G279medium positional0.370.5
28H279medium positional0.440.5
31A311medium positional0.270.5
32B311medium positional0.510.5
33C311medium positional0.380.5
34D311medium positional0.440.5
35E311medium positional0.520.5
36F311medium positional0.330.5
37G311medium positional0.520.5
38H311medium positional0.410.5
41A117medium positional0.480.5
42B117medium positional0.210.5
43C117medium positional0.350.5
44D117medium positional0.280.5
45E117medium positional0.450.5
46F117medium positional0.220.5
47G117medium positional0.320.5
48H117medium positional0.340.5
11A324tight thermal0.080.5
12B324tight thermal0.070.5
13C324tight thermal0.080.5
14D324tight thermal0.070.5
15E324tight thermal0.080.5
16F324tight thermal0.080.5
17G324tight thermal0.070.5
18H324tight thermal0.090.5
21A312tight thermal0.090.5
22B312tight thermal0.090.5
23C312tight thermal0.110.5
24D312tight thermal0.090.5
25E312tight thermal0.10.5
26F312tight thermal0.110.5
27G312tight thermal0.110.5
28H312tight thermal0.110.5
31A348tight thermal0.120.5
32B348tight thermal0.120.5
33C348tight thermal0.130.5
34D348tight thermal0.110.5
35E348tight thermal0.120.5
36F348tight thermal0.130.5
37G348tight thermal0.130.5
38H348tight thermal0.120.5
41A112tight thermal0.080.5
42B112tight thermal0.090.5
43C112tight thermal0.080.5
44D112tight thermal0.080.5
45E112tight thermal0.070.5
46F112tight thermal0.080.5
47G112tight thermal0.090.5
48H112tight thermal0.080.5
11A304medium thermal0.532
12B304medium thermal0.552
13C304medium thermal0.642
14D304medium thermal0.442
15E304medium thermal0.512
16F304medium thermal0.522
17G304medium thermal0.532
18H304medium thermal0.542
21A279medium thermal0.682
22B279medium thermal0.632
23C279medium thermal0.712
24D279medium thermal0.652
25E279medium thermal0.662
26F279medium thermal0.82
27G279medium thermal0.692
28H279medium thermal0.712
31A311medium thermal0.72
32B311medium thermal0.792
33C311medium thermal0.792
34D311medium thermal0.742
35E311medium thermal0.822
36F311medium thermal0.772
37G311medium thermal0.872
38H311medium thermal0.842
41A117medium thermal0.512
42B117medium thermal0.542
43C117medium thermal0.742
44D117medium thermal0.532
45E117medium thermal0.662
46F117medium thermal0.492
47G117medium thermal0.562
48H117medium thermal0.522
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 701 -
Rwork0.25 13871 -
obs--94.82 %
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)
11.6643-0.07790.0560.6811-0.24590.17370.0007-0.20060.50940.11030.0188-0.0469-0.1149-0.0093-0.0195-0.0493-0.00390.0103-0.1514-0.11120.071359.875114.69931.156
21.3625-0.2482-0.33580.91930.13210.51730.0319-0.0840.31340.03460.0084-0.1615-0.07530.0803-0.0402-0.1129-0.02170.0015-0.1669-0.018-0.038975.902103.04921.993
31.6712-0.0629-0.05370.13780.02250.72240.01510.2807-0.1464-0.0941-0.01030.01820.0925-0.0365-0.0048-0.06870.0032-0.0011-0.1038-0.0305-0.183240.14572.435-2.097
41.12450.03280.480.85710.06480.5289-0.0194-0.1490.41230.06830.02660.059-0.1093-0.1242-0.0071-0.08240.00760.0322-0.1485-0.08710.054538.05114.07730.473
50.9241-0.05320.22370.66430.26550.3743-0.0011-0.02420.2748-0.01580.03260.0938-0.0293-0.0777-0.0316-0.10870.00310.0193-0.1482-0.0012-0.05823.241101.42320.402
61.1316-0.3916-0.26540.65270.130.9869-0.00920.14660.0071-0.0578-0.02610.12310.0534-0.10350.0352-0.1202-0.0082-0.0186-0.13420.006-0.151424.13284.1587.001
70.95510.3743-0.01230.5960.22980.4584-0.00170.14240.0843-0.011-0.008-0.1520.00390.04640.0097-0.10620.0040.0203-0.1320.0065-0.141976.77885.9418.414
81.66750.68360.06140.78320.0110.6699-0.00750.2572-0.1334-0.07490.0109-0.1260.07220.0728-0.0033-0.0970.01490.0261-0.102-0.0364-0.177761.97473.165-1.535
910.0831-0.64852.0315-1.49413.11590.0117-0.47580.23490.2632-0.0902-0.213-0.34190.10630.07860.0304-0.0418-0.05690.0926-0.1197-0.116263.26191.52659.893
101.3295-0.6012-0.19363.1871-0.68031.75970.0169-0.702-0.21980.35140.0136-0.0409-0.05470.0314-0.03040.1829-0.0842-0.03590.53670.0369-0.195153.40471.17783.793
110.69490.36990.13071.3996-1.41743.9211-0.0491-0.19410.02550.0905-0.1962-0.3537-0.07160.36490.2452-0.0687-0.0197-0.0505-0.01370.0298-0.096978.08577.97749.298
121.01630.3381-0.54153.9468-0.99981.8854-0.0248-0.5827-0.25060.42350.0233-0.11980.07040.02130.00150.1117-0.0545-0.10580.38620.1388-0.126770.24963.27177.668
131.7904-0.40880.65041.8489-1.23982.33580.00120.0122-0.2417-0.25610.02460.05540.1975-0.1744-0.0259-0.0622-0.0299-0.0064-0.19180.041-0.109936.48850.00627.114
142.2958-0.7110.10190.9325-0.62432.0080.0807-0.5009-0.44780.0884-0.03370.0885-0.0443-0.012-0.0471-0.0203-0.0448-0.0327-0.03720.26450.122746.17931.51252.551
151.37550.2892-1.01232.1945-1.9042.78950.1214-0.40570.31780.4162-0.0638-0.024-0.4186-0.0388-0.05750.0605-0.02650.01870.1116-0.1343-0.141940.5992.95660.893
162.0054-0.69860.96873.2196-1.27221.03450.0251-0.7453-0.12150.36620.0113-0.0336-0.0334-0.0574-0.03640.1595-0.06680.08220.4870.0737-0.180534.43267.47280.758
171.4230.4107-0.25542.893-2.22621.89310.0184-0.27580.2570.28940.11490.293-0.2479-0.2785-0.1334-0.0118-0.00180.06660.0499-0.0487-0.170523.36381.41151.707
181.7153-0.80911.27882.1987-1.17762.54430.0429-0.6783-0.15660.31910.0456-0.01020.033-0.0351-0.08840.0464-0.0440.09080.3150.1763-0.083924.46354.29270.367
190.89130.00770.36042.6886-1.84122.2163-0.0488-0.1453-0.07770.02130.2410.3206-0.0765-0.3362-0.1922-0.1027-0.01550.0342-0.09060.0585-0.13621.71363.54237.698
201.5849-0.4039-0.10181.8519-0.79513.66170.0378-0.5691-0.34330.27390.00120.1352-0.00410.0286-0.0389-0.0347-0.04640.02540.07080.25610.04129.3339.41658.666
211.6654-0.36790.82551.3748-1.87343.46360.045-0.004-0.1906-0.2093-0.2104-0.34340.30350.22990.1654-0.05660.01440.005-0.15640.0753-0.043676.43660.21635.308
221.31360.7572-0.17842.1972-0.8332.46760.1123-0.4834-0.4110.2829-0.0966-0.13440.0739-0.0723-0.01580.0148-0.0487-0.12280.19480.2590.033575.14748.38265.97
231.355-0.46490.66541.9032-1.84633.10280.09280.073-0.3628-0.3596-0.0572-0.0460.3565-0.0234-0.0357-0.03990.00320.009-0.21060.0195-0.054459.22248.55326.125
242.62060.9019-0.40131.0475-0.48283.12130.1064-0.4786-0.42790.2067-0.1053-0.14790.12-0.1109-0.0012-0.0163-0.0319-0.04890.0110.26640.104765.15535.18255.512
2514.624-4.934822.66165.0337-13.462347.1447-0.23710.13760.5855-0.90660.15480.19520.9095-0.62320.08230.19320.0169-0.0068-0.00610.27520.307641.345124.001-6.422
2618.9645-17.095718.511422.9696-23.931326.24450.16340.26160.4155-0.46350.15190.48950.2232-0.4813-0.31530.09850.01080.02370.02180.24010.334851.674126.57-4.61
2715.225718.8386-8.607251.4484-27.333816.4249-0.58270.92770.47110.36340.7549-0.4912-0.92940.0375-0.17220.2005-0.04310.01340.25580.1978-0.022258.789106.589-19.99
280.19280.4314-1.14232.2562-7.940270.3745-0.25610.34360.073-0.5038-0.5903-0.0686-0.22470.36640.84640.13920.046-0.03570.11560.24360.300836.166116.669-12.241
2913.38856.3606-22.4574.884-15.098655.49580.4970.75780.3203-0.1593-0.2264-0.0618-0.030.187-0.27050.12050.0413-0.0480.15910.2740.107339.187108.463-18.675
3017.162814.7968-18.924917.3085-20.236126.95830.03141.04650.18510.09980.1258-0.181-0.4122-0.0119-0.15720.08280.0249-0.02020.24990.21750.011948.464104.303-22.012
317.815-16.64128.050949.6282-24.267912.58080.31860.12330.6592-0.5375-0.0431-0.2344-0.002-0.1455-0.27550.1394-0.02280.02890.05620.24830.277561.048122.301-7.666
320.2192-0.7955-0.551457.5537-15.62987.073-0.08730.19840.4715-0.41410.6073-0.2164-0.3992-0.368-0.520.105-0.00090.05170.21930.29420.181764.124114.077-14.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 64
2X-RAY DIFFRACTION1A252 - 354
3X-RAY DIFFRACTION2B21 - 64
4X-RAY DIFFRACTION2B252 - 354
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