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- PDB-4wgl: Crystal structure of a GroEL D83A/R197A double mutant -

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Basic information

Entry
Database: PDB / ID: 4wgl
TitleCrystal structure of a GroEL D83A/R197A double mutant
Components60 kDa chaperonin
KeywordsCHAPERONE / chaperonin / protein folding
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsYang, D. / Fei, X. / LaRonde, N.A. / Beckett, D. / Lund, P.A. / Lorimer, G.H.
CitationJournal: To Be Published
Title: Crystal structure of a GroEL D83A/R197A double mutant
Authors: Yang, D. / Fei, X. / LaRonde, N.A. / Beckett, D. / Lund, P.A. / Lorimer, G.H.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 60 kDa chaperonin
B: 60 kDa chaperonin
C: 60 kDa chaperonin
D: 60 kDa chaperonin
E: 60 kDa chaperonin
F: 60 kDa chaperonin
G: 60 kDa chaperonin
H: 60 kDa chaperonin
I: 60 kDa chaperonin
J: 60 kDa chaperonin
K: 60 kDa chaperonin
L: 60 kDa chaperonin
M: 60 kDa chaperonin
N: 60 kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)801,66214
Polymers801,66214
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47720 Å2
ΔGint-224 kcal/mol
Surface area291350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.619, 259.710, 280.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
60 kDa chaperonin / GroEL protein / Protein Cpn60


Mass: 57261.578 Da / Num. of mol.: 14 / Mutation: D83A, R197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: groL, groEL, mopA, b4143, JW4103 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6F5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 25% PEG 3000, 0.1M acetic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.13→190.68 Å / Num. obs: 174190 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.138 / Rsym value: 0.153 / Net I/σ(I): 10.2
Reflection shellResolution: 3.13→3.31 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1xck
Resolution: 3.13→123.524 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 2003 1.15 %
Rwork0.1655 --
obs0.1663 174035 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.13→123.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53844 0 0 0 53844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00954236
X-RAY DIFFRACTIONf_angle_d1.22173248
X-RAY DIFFRACTIONf_dihedral_angle_d16.16820398
X-RAY DIFFRACTIONf_chiral_restr0.0488932
X-RAY DIFFRACTIONf_plane_restr0.0059590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.20830.33071350.251812181X-RAY DIFFRACTION100
3.2083-3.2950.29591510.216812192X-RAY DIFFRACTION100
3.295-3.3920.27581280.20512221X-RAY DIFFRACTION100
3.392-3.50150.27821520.194812186X-RAY DIFFRACTION100
3.5015-3.62660.26371440.191912191X-RAY DIFFRACTION100
3.6266-3.77190.25531440.181612199X-RAY DIFFRACTION100
3.7719-3.94350.23921300.166712276X-RAY DIFFRACTION100
3.9435-4.15150.21671560.150512232X-RAY DIFFRACTION100
4.1515-4.41160.21741390.139312258X-RAY DIFFRACTION100
4.4116-4.75220.22051370.137412253X-RAY DIFFRACTION100
4.7522-5.23040.19591500.137612326X-RAY DIFFRACTION100
5.2304-5.98730.23471470.166712384X-RAY DIFFRACTION100
5.9873-7.54320.23451390.174212427X-RAY DIFFRACTION99
7.5432-123.62010.19851510.151412706X-RAY DIFFRACTION99
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)
10.11370.1496-0.01390.22850.02490.1121-0.04380.11770.1399-0.05810.08150.27840.0382-0.02230.04420.1570.03670.00170.1498-0.0641-0.088428.9363-0.30819.2409
20.0936-0.00820.01320.0649-0.00150.0440.0934-0.05690.0814-0.27720.07910.17430.2217-0.12030.00140.5631-0.0487-0.10250.49280.04950.327725.22473.4384-13.0104
30.08750.0213-0.11710.1391-0.07840.1845-0.0692-0.04980.0925-0.03980.006-0.08310.02130.069-0.08010.1618-0.0025-0.02630.181-0.00670.128137.93090.65118.5196
40.1131-0.02150.01850.1457-0.09580.12020.02840.11940.0543-0.0936-0.06460.026-0.01840.0229-0.05010.15270.01510.00260.1244-0.0330.138114.2595-30.686524.6269
50.2282-0.0598-0.20340.06710.02960.252-0.44530.20160.3229-0.12190.0624-0.0165-0.08190.2723-0.30010.3929-0.2334-0.21770.28930.06490.066719.2554-39.699-5.7967
60.11850.04580.02320.032-0.03980.11830.01920.03450.00540.013-0.01250.06290.10990.0928-0.0440.24670.0321-0.03860.221-0.01490.153120.755-41.415928.6754
70.1251-0.0466-0.11030.1211-0.01320.12850.08820.11830.0545-0.0742-0.04470.00120.05370.08810.13650.21020.006-0.08250.2048-0.04590.1423-21.3539-49.120420.197
80.04940.0083-0.02730.0274-0.00110.0108-0.12530.35880.3437-0.0412-0.07-0.09160.0345-0.2287-0.00010.63390.025-0.14970.93210.0940.8607-16.519-46.9343-11.4013
90.11630.0372-0.02640.06970.02490.0932-0.03450.0615-0.1730.0586-0.1161-0.060.0566-0.0575-0.35510.13310.0136-0.11030.1743-0.09420.0369-22.6703-57.935220.0577
100.04670.0417-0.06780.0887-0.05980.14480.04810.00980.0331-0.04580.11960.02410.04740.03590.11650.06280.0069-0.04670.0921-0.00910.1081-45.0716-19.600124.9485
110.0674-0.0482-0.01090.0631-0.00210.01880.02490.0221-0.0193-0.0708-0.0024-0.01160.08330.0337-0.01020.14090.0223-0.02680.2059-0.01640.0911-50.019-35.376126.384
120.0283-0.03870.03850.0354-0.04150.06270.20880.0426-0.0312-0.1956-0.1910.03230.134-0.0839-0.0010.63990.2073-0.06510.70810.07360.4027-56.9537-25.5892-1.9589
13-0.00190.00130.0070.0004-0.00070.00850.0729-0.02820.0289-0.00910.0621-0.04270.05180.03740.00011.13570.14930.0161.02090.04870.9653-39.3168-24.4651-2.9503
140.05060.01030.00970.02050.00220.0440.19560.04750.0234-0.1997-0.04120.074-0.04490.00940.00230.79810.3232-0.09950.96650.00190.3974-54.4524-35.6457-12.2129
150.0628-0.03160.03130.0572-0.00280.1827-0.01350.0121-0.1161-0.0247-0.06120.11790.1452-0.1401-0.12930.07440.0149-0.09460.1803-0.03630.1702-61.3693-31.118525.8348
160.06590.01170.00830.02440.0070.01870.03750.04470.09490.0079-0.0479-0.06030.01330.10180.03550.14630.0176-0.02820.202-0.00340.2229-49.54667.424825.1164
170.06730.08190.05140.3220.04510.0655-0.06990.0984-0.09620.02760.0186-0.37-0.08330.03350.12410.2521-0.02510.07820.42030.07960.4095-59.35859.0304-3.1174
180.12730.03340.16570.1130.0430.1523-0.1082-0.00560.13790.02740.1343-0.06850.0045-0.12310.0140.18590.010.00980.29380.04160.2611-65.712114.399720.7711
190.0378-0.00740.03090.08030.05580.14430.0690.1149-0.0664-0.0398-0.0401-0.0085-0.0455-0.12520.00810.2161-0.0061-0.0310.2404-0.00390.2849-31.006132.151625.5641
200.0572-0.0536-0.03250.03290.04160.0331-0.0632-0.00190.0828-0.02840.18660.113-0.04970.022200.6393-0.07560.03280.71660.14230.5649-31.470939.6531-6.6938
210.0722-0.01080.04630.03410.02170.1715-0.01530.0290.13540.0271-0.06360.017-0.1232-0.2189-0.11120.12810.0379-0.01060.08670.04730.2271-31.170546.407725.7713
220.0885-0.00290.06620.07790.00180.086-0.0027-0.039-0.069-0.08120.02540.0204-0.0465-0.04840.06880.1547-0.0037-0.03170.1584-0.02590.16963.375130.508124.8402
230.0155-0.01720.00620.0088-0.01880.02970.19990.1734-0.10330.0161-0.09650.24190.02260.0529-0.00010.56530.1809-0.02570.7548-0.01960.61718.862136.2276-8.1936
240.1369-0.04120.11170.0686-0.03420.1213-0.0454-0.02280.134-0.0946-0.0129-0.0969-0.1360.0025-0.03190.2054-0.0255-0.00690.2053-0.03040.256614.401839.562824.5952
250.0619-0.0101-0.03850.06380.0380.07780.0336-0.04070.06720.0313-0.0001-0.05520.0229-0.03340.05130.11660.0176-0.03850.12160.00770.1418-33.5942-39.631962.1276
260.06590.0099-0.07340.08190.02730.03270.0641-0.06340.00240.0781-0.00990.0250.08540.060400.406-0.0112-0.06950.42340.10130.3064-33.4793-47.209294.8162
270.1343-0.0314-0.07350.10790.01090.11150.07080.0119-0.0599-0.0135-0.10820.01920.0456-0.0407-0.09920.1429-0.0275-0.04760.12680.04980.1974-34.8663-53.822662.0166
280.0707-0.0248-0.01690.03610.02330.10740.0377-0.01510.0790.0374-0.0163-0.07210.0177-0.01720.02120.11420.0072-0.02590.13230.01340.16770.7004-40.374961.7727
290.07210.0743-0.0140.1228-0.0150.09570.12170.0270.4106-0.0034-0.02990.6382-0.16010.22310.14830.2395-0.1920.0329-0.0646-0.13830.75076.5828-41.743395.4703
300.0550.06560.01390.116-0.13840.06180.19430.3121-0.2073-0.0618-0.17130.09210.04490.0518-0.0210.0241-0.1424-0.0138-0.24020.06410.107310.0618-52.093471.3219
310.0534-0.01710.02860.185-0.01470.1257-0.06740.0088-0.02580.02720.09280.1161-0.03520.03360.17270.1628-0.00880.00060.1413-0.03280.09529.2466-12.149765.9761
320.0429-0.02930.00830.07540.03360.05560.0304-0.074-0.0523-0.0536-0.02880.1677-0.0886-0.04470.08880.5015-0.22230.10880.2409-0.18030.157425.457-13.879198.7956
330.22830.04030.05020.2656-0.06870.09480.00890.11060.08780.1635-0.00080.0353-0.03590.05970.07680.1036-0.0235-0.00750.02540.00980.037738.9001-14.991369.999
340.03340.0026-0.03080.0364-0.02820.01590.0523-0.04770.0482-0.0143-0.04470.1094-0.01770.0009-0.01620.193-0.0045-0.01680.1087-0.00230.187312.764618.966961.9512
350.2044-0.06590.07180.15490.1130.2211-0.2369-0.1021-0.2930.16910.27760.13850.01610.32430.06440.47210.31640.04650.102-0.04590.207923.969225.025492.1432
360.0875-0.08970.0720.07770.02850.0574-0.04970.0020.10110.06930.0095-0.04550.03730.0976-0.08570.1359-0.0166-0.01740.0743-0.04810.100625.754831.41266.1049
370.1732-0.01130.07940.0726-0.04990.07770.1010.0205-0.1440.0535-0.10710.0034-0.03630.0225-0.00830.1722-0.0343-0.00380.1134-0.01830.1717-17.045940.098967.1877
380.1197-0.0002-0.03930.09730.0050.0612-0.0442-0.1511-0.3034-0.01210.1476-0.19960.2022-0.19110.07030.4873-0.1509-0.03910.40120.05080.4741-12.036235.710497.3439
390.10970.09310.05350.11790.06880.05880.0488-0.1513-0.0723-0.0796-0.1157-0.05250.0328-0.0098-0.1186-0.0029-0.1715-0.0776-0.1889-0.13510.087-17.842448.748567.3532
400.06820.01270.03310.06720.0130.0673-0.0212-0.0249-0.03850.04950.0156-0.0791-0.08050.003-0.00960.2429-0.0249-0.01090.228-0.02970.301-45.032221.2562.4754
410.06630.001-0.04590.1190.00950.01250.225-0.2355-0.16910.1438-0.3073-0.0770.1151-0.0384-0.00390.5448-0.14740.01970.62120.16830.4619-51.674424.554695.8397
420.08130.0056-0.01290.0690.0460.1271-0.0530.02540.13440.1325-0.02090.1371-0.0781-0.0539-0.02740.21150.01820.04390.2172-0.00120.3516-58.500425.845162.7148
430.13480.00210.02150.08530.04960.1415-0.0482-0.13580.0531-0.03040.0212-0.052-0.0778-0.00590.00910.0952-0.0073-0.01840.08770.00150.1009-53.8787-11.957562.6271
440.1165-0.0721-0.07580.04580.05930.03890.19370.04830.04650.14740.088-0.30380.0649-0.08530.00390.53250.0078-0.06850.31040.01390.4091-58.7537-15.424995.5527
450.1273-0.004-0.04510.15180.02720.14-0.0566-0.025-0.0265-0.0566-0.0126-0.08250.0094-0.0277-0.19240.1281-0.0019-0.01020.1820.01270.1603-65.7958-19.558562.9244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 179 )
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 355 )
3X-RAY DIFFRACTION3chain 'A' and (resid 356 through 525 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 134 )
5X-RAY DIFFRACTION5chain 'B' and (resid 135 through 433 )
6X-RAY DIFFRACTION6chain 'B' and (resid 434 through 525 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 179 )
8X-RAY DIFFRACTION8chain 'C' and (resid 180 through 358 )
9X-RAY DIFFRACTION9chain 'C' and (resid 359 through 525 )
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 64 )
11X-RAY DIFFRACTION11chain 'D' and (resid 65 through 134 )
12X-RAY DIFFRACTION12chain 'D' and (resid 135 through 255 )
13X-RAY DIFFRACTION13chain 'D' and (resid 256 through 281 )
14X-RAY DIFFRACTION14chain 'D' and (resid 282 through 385 )
15X-RAY DIFFRACTION15chain 'D' and (resid 386 through 525 )
16X-RAY DIFFRACTION16chain 'E' and (resid 2 through 109 )
17X-RAY DIFFRACTION17chain 'E' and (resid 110 through 358 )
18X-RAY DIFFRACTION18chain 'E' and (resid 359 through 525 )
19X-RAY DIFFRACTION19chain 'F' and (resid 2 through 134 )
20X-RAY DIFFRACTION20chain 'F' and (resid 135 through 385 )
21X-RAY DIFFRACTION21chain 'F' and (resid 386 through 525 )
22X-RAY DIFFRACTION22chain 'G' and (resid 2 through 134 )
23X-RAY DIFFRACTION23chain 'G' and (resid 135 through 385 )
24X-RAY DIFFRACTION24chain 'G' and (resid 386 through 525 )
25X-RAY DIFFRACTION25chain 'H' and (resid 2 through 134 )
26X-RAY DIFFRACTION26chain 'H' and (resid 135 through 385 )
27X-RAY DIFFRACTION27chain 'H' and (resid 386 through 525 )
28X-RAY DIFFRACTION28chain 'I' and (resid 2 through 134 )
29X-RAY DIFFRACTION29chain 'I' and (resid 135 through 338 )
30X-RAY DIFFRACTION30chain 'I' and (resid 339 through 525 )
31X-RAY DIFFRACTION31chain 'J' and (resid 2 through 179 )
32X-RAY DIFFRACTION32chain 'J' and (resid 180 through 338 )
33X-RAY DIFFRACTION33chain 'J' and (resid 339 through 525 )
34X-RAY DIFFRACTION34chain 'K' and (resid 2 through 109 )
35X-RAY DIFFRACTION35chain 'K' and (resid 110 through 358 )
36X-RAY DIFFRACTION36chain 'K' and (resid 359 through 525 )
37X-RAY DIFFRACTION37chain 'L' and (resid 2 through 179 )
38X-RAY DIFFRACTION38chain 'L' and (resid 180 through 358 )
39X-RAY DIFFRACTION39chain 'L' and (resid 359 through 525 )
40X-RAY DIFFRACTION40chain 'M' and (resid 2 through 134 )
41X-RAY DIFFRACTION41chain 'M' and (resid 135 through 385 )
42X-RAY DIFFRACTION42chain 'M' and (resid 386 through 525 )
43X-RAY DIFFRACTION43chain 'N' and (resid 2 through 134 )
44X-RAY DIFFRACTION44chain 'N' and (resid 135 through 385 )
45X-RAY DIFFRACTION45chain 'N' and (resid 386 through 525 )

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