[English] 日本語
Yorodumi
- PDB-4wsc: Crystal structure of a GroELK105A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wsc
TitleCrystal structure of a GroELK105A mutant
Components60 kDa chaperonin
KeywordsCHAPERONE / chaperonin / helix dipole / negative cooperativity
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: 3.04 Å
AuthorsLorimer, G.H. / Ye, X. / Fei, X. / Yang, D. / Corsepius, N. / LaRonde, N.A.
CitationJournal: To Be Published
Title: Crystal structure of a GroELK105A mutant
Authors: Lorimer, G.H. / Ye, X. / Fei, X. / Yang, D. / Corsepius, N. / LaRonde, N.A.
History
DepositionOct 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)802,67114
Polymers802,67114
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49360 Å2
ΔGint-212 kcal/mol
Surface area288090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.640, 259.390, 143.310
Angle α, β, γ (deg.)90.00, 105.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 57333.609 Da / Num. of mol.: 14 / Mutation: K105A
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 4000, HEPES / PH range: 6.5-7.5

-
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: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.04→84.15 Å / Num. obs: 180177 / % possible obs: 98.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 6.9
Reflection shellResolution: 3.04→3.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2 / % possible all: 95.2

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1xck
Resolution: 3.04→80.523 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 2001 1.11 %
Rwork0.19 --
obs0.1908 180102 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.04→80.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53914 0 0 0 53914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154306
X-RAY DIFFRACTIONf_angle_d1.42273346
X-RAY DIFFRACTIONf_dihedral_angle_d14.71720440
X-RAY DIFFRACTIONf_chiral_restr0.0598932
X-RAY DIFFRACTIONf_plane_restr0.0079618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.1160.33881400.272412318X-RAY DIFFRACTION95
3.116-3.20030.3721290.264412310X-RAY DIFFRACTION96
3.2003-3.29450.321450.255612452X-RAY DIFFRACTION97
3.2945-3.40080.32671460.248212534X-RAY DIFFRACTION97
3.4008-3.52240.30411410.218512598X-RAY DIFFRACTION98
3.5224-3.66340.26711350.207212633X-RAY DIFFRACTION98
3.6634-3.83010.261540.192912751X-RAY DIFFRACTION99
3.8301-4.0320.24141400.173212804X-RAY DIFFRACTION99
4.032-4.28460.22521450.166912870X-RAY DIFFRACTION100
4.2846-4.61540.22791480.159912956X-RAY DIFFRACTION100
4.6154-5.07980.22841440.157912925X-RAY DIFFRACTION100
5.0798-5.81470.25271410.175812940X-RAY DIFFRACTION100
5.8147-7.32520.23671460.181512953X-RAY DIFFRACTION100
7.3252-80.55140.1911470.149713057X-RAY DIFFRACTION100
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)
12.1133-0.0699-0.23870.32040.04540.2431-0.02070.10110.1030.00860.06170.1413-0.0564-0.0596-0.03730.16420.0431-0.02240.1526-0.01420.199254.471710.81267.1611
21.36620.18350.03013.24580.12590.54180.29430.33760.5455-0.7122-0.18931.4981-0.0005-0.0335-0.09720.53720.1718-0.08580.4426-0.06470.969460.12387.2588-26.3413
31.0412-0.365-0.41691.39280.35530.8498-0.02090.0014-0.08110.06020.0664-0.11860.1396-0.052-0.02690.1398-0.0015-0.00860.16370.02450.287966.49593.1546.9096
40.86120.18820.10240.92470.10730.42740.11080.03590.0873-0.0814-0.0642-0.09230.05240.0298-0.04120.13940.0077-0.00590.17910.00220.207132.9923-23.05582.6855
54.29030.87410.24813.5361-0.24081.82670.1010.15140.4088-0.27240.1118-0.2969-0.16740.2171-0.1820.3768-0.01380.05940.3373-0.02950.232134.5056-17.8321-27.3066
60.69240.62830.13930.9732-0.12670.28860.094-0.0021-0.03690.0732-0.0381-0.02360.06060.0515-0.04920.13270.0116-0.00860.1952-0.01630.193236.5197-31.25992.1561
73.1165-0.39630.2560.1245-0.20670.77990.16770.34040.17010.0494-0.17870.3217-0.27560.230.0060.1249-0.04250.04140.0782-0.05020.348-2.0787-9.22727.6464
80.1955-0.27420.08281.0390.34530.88550.06650.1411-0.165-0.0511-0.0429-0.0052-0.00750.1744-0.01360.11760.0353-0.00860.18260.03970.1877-8.1794-26.87310.401
93.11830.0901-0.7271.7440.43730.92880.06640.26390.5738-0.13850.0813-0.122-0.23880.0593-0.0430.33960.02080.06510.17950.01830.3058-2.3317-20.4067-27.1237
101.2023-0.05960.62730.78860.13431.18240.0168-0.1130.0363-0.01470.00050.17150.0411-0.1586-0.01880.1399-0.01840.04240.1268-0.02610.1757-10.637-27.23978.0629
110.8469-1.13840.05621.7176-0.50140.8204-0.05680.12030.2342-0.06380.1857-0.1809-0.14330.23930.07840.0959-0.0296-0.01710.122-0.03560.5065-17.418115.21418.1583
120.8362-0.26870.2940.86970.50830.69310.17140.4354-0.1085-0.2148-0.1010.2918-0.02780.1772-0.03270.21410.09630.0190.22020.07340.4283-35.04368.32551.461
133.5013-0.8046-0.53023.95731.3120.63260.32370.4930.1721-0.4588-0.1784-0.9511-0.08490.0361-0.04030.58740.14820.06730.45170.16490.4738-27.15547.979-27.1248
142.4805-0.4011-0.31060.85020.38561.1534-0.1806-0.1340.051-0.08280.17880.2272-0.0733-0.12280.10750.11380.0172-0.01830.138-0.01450.2372-36.729710.16549.1948
151.67320.8091-0.95762.9126-0.37910.96270.18910.0456-0.0358-0.2136-0.2223-0.15230.1210.16310.00280.1844-0.0391-0.07360.12110.02280.2972-12.213641.8738.1919
162.73811.3460.47410.95460.02460.2378-0.08442.0181-0.4187-0.58810.1486-0.0167-0.05480.4214-0.15290.5657-0.2725-0.06150.44780.20070.8435-22.137347.7876-20.5433
170.968-0.15710.52122.0993-0.08530.4804-0.05070.18870.2582-0.121-0.02220.3644-0.1276-0.00810.04420.2370.009-0.00740.21860.1220.5284-25.07254.24454.3735
181.71570.1054-0.13321.37470.01170.57390.0024-0.0394-0.27990.04880.00350.03040.0716-0.0127-0.01450.1217-0.01460.02070.16890.04960.274914.043157.75488.2008
192.2581-1.04850.33871.69160.07450.6176-0.14390.2563-1.0522-0.07570.09730.14880.22860.0776-0.01220.39010.04480.1580.3807-0.05120.685515.685563.9441-24.6771
201.1587-0.10650.21881.3591-0.06420.95940.0752-0.0693-0.0542-0.0615-0.0888-0.0599-0.03770.13540.01170.13330.0642-0.00850.12540.05410.28518.96471.01818.0916
211.8701-0.4908-0.04161.37320.26880.6186-0.21270.0524-0.2131-0.07360.2970.1981-0.13480.07910.06960.11870.05280.04930.17280.07780.341644.397539.82266.6868
220.44680.28510.11530.20710.48431.99090.02430.12820.3363-0.15730.2035-0.358-0.30590.5557-0.12210.27550.12340.07490.38470.04250.461263.333351.7211-4.1987
233.9403-0.43920.43362.1964-0.24690.89340.31390.359-0.1841-0.0995-0.13270.5446-0.1726-0.0717-0.15470.44960.20320.09540.5330.07270.586448.061746.9044-28.0451
241.7698-0.9938-0.61841.61030.10640.62890.0038-0.13790.2311-0.17730.0807-0.31490.01970.2096-0.04220.20910.01170.02040.21070.07470.35959.19448.59437.2479
252.8830.8014-0.71171.2057-0.32770.3218-0.1498-0.0643-0.14030.16410.06120.11860.0784-0.00040.04770.1313-0.02470.02570.2652-0.03760.2805-2.816848.736946.1448
260.84220.4499-1.15640.8769-1.33582.0422-0.0824-0.00430.15570.37340.33520.2273-0.1294-0.2477-0.19590.36150.03440.1720.39650.0150.6256-16.407166.308258.0004
274.66131.9382-0.0923.61390.0550.5090.5701-0.43870.41730.5121-0.1473-0.2833-0.27680.3841-0.36930.6034-0.18210.10490.7509-0.13090.4411-2.811955.621380.1656
281.97110.7214-0.40360.65680.27881.44410.0574-0.01050.13070.1232-0.03250.3655-0.1274-0.2254-0.05430.22270.02280.0910.2153-0.01350.4116-13.648462.039545.9969
291.39431.481-0.36523.9947-0.36321.0058-0.0407-0.31470.1523-0.01920.21110.2567-0.01020.0652-0.05670.1226-0.0253-0.00540.29170.02160.271-16.938218.94146.1323
301.3376-0.3418-0.76971.0450.03411.7711-0.09530.03870.00890.11190.22780.0445-0.021-0.2624-0.1270.1556-0.037-0.00490.250.02610.1516-34.740424.327653.368
312.32880.331-0.09822.6060.34511.08170.203-0.16050.11950.3832-0.0834-0.27940.09920.0534-0.0960.4001-0.0068-0.01150.56640.07880.2748-25.482525.12680.9209
321.71910.3968-0.09921.23490.62270.7828-0.05840.09540.12360.00880.02960.1502-0.0121-0.01060.00180.15330.03750.01180.23850.03240.1744-36.620722.339345.7548
331.5313-1.9652-0.00274.150.00980.45020.13530.06490.1917-0.0816-0.1398-0.1670.12610.11180.02730.1528-0.00240.03710.27520.03870.1992-5.2835-7.408645.6468
341.09490.1756-0.44490.61020.04341.26510.0087-0.24980.02890.19580.00840.20950.0474-0.23720.030.3055-0.0159-0.01590.27930.00880.1747-20.9589-18.367952.517
352.05350.11370.18092.35590.60241.5566-0.091-0.02240.3180.10950.17720.0640.0598-0.009-0.03660.45390.03820.03790.53950.20050.2692-17.0628-11.614180.4409
361.57360.1507-0.17381.81330.34260.8973-0.0689-0.0515-0.2341-0.04120.09110.29180.2438-0.1587-0.01110.1918-0.03440.02020.21560.01570.2211-20.3541-20.740744.9206
371.6458-0.3634-0.64651.70660.05450.29820.137-0.08250.15150.1512-0.06150.00270.0962-0.1371-0.03180.19290.0318-0.03410.2543-0.01480.233317.8429-21.499344.7291
381.8692-0.5009-1.00471.13811.07551.5745-0.0859-0.16360.33180.19670.0957-0.01330.1927-0.0478-0.02750.37240.023-0.0360.53810.10470.43120.8004-29.81778.4359
391.4416-0.362-0.27060.993-0.32520.4104-0.0891-0.0916-0.21680.1457-0.04010.00880.02540.09760.07750.238-0.01950.01030.21290.01750.198423.7246-34.470544.6473
402.35650.4675-0.32951.99720.47270.9823-0.06370.0470.19750.18880.14860.15140.24060.0197-0.08470.2032-0.0330.02630.25130.00160.189848.1765-5.275444.3152
411.95722.08690.36553.1386-0.0491.02720.8208-1.05920.40180.8458-0.83631.16180.0212-0.2154-0.02570.6595-0.29220.10641.1204-0.17381.055755.5728-8.13177.8007
422.57770.799-0.08071.62080.24981.1011-0.16450.0658-0.37590.05520.1844-0.36590.10010.2135-0.00120.20650.04260.00710.21520.00820.320261.9292-8.780844.2001
432.4208-0.11550.22621.4712-0.51760.41830.016-0.1484-0.1061-0.00560.04120.30670.039-0.0204-0.04910.1961-0.01-0.01420.2403-0.06120.225954.375328.579144.2249
441.5821-0.9454-0.09362.6695-0.88691.3164-0.1486-0.5958-0.16340.51840.37060.5689-0.2377-0.2127-0.16080.46840.17030.04980.7622-0.050.377460.571832.706577.1291
451.07030.1052-0.00921.41340.47881.2015-0.0286-0.19770.20860.02840.1705-0.1033-0.14870.0845-0.1730.21540.0158-0.00110.3012-0.05240.205665.788437.194343.9975
461.94390.64460.17322.1611-0.50250.74220.0253-0.13720.06430.15050.0572-0.04250.02170.2028-0.01980.15610.05090.00570.3012-0.06570.205631.891554.680444.7028
472.3482-0.55310.63861.4160.02741.0739-0.1888-0.5027-0.54070.65210.29220.59750.0097-0.1224-0.10820.6690.12340.280.6508-0.05250.69331.346659.742376.878
481.5513-0.430.46541.1660.30950.9378-0.0217-0.2140.41170.17190.0007-0.0471-0.14340.007-0.08470.2292-0.04770.13210.2829-0.08030.502534.853269.624253.7349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 134 )
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 385 )
3X-RAY DIFFRACTION3chain 'A' and (resid 386 through 525 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 179 )
5X-RAY DIFFRACTION5chain 'B' and (resid 180 through 355 )
6X-RAY DIFFRACTION6chain 'B' and (resid 356 through 525 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 64 )
8X-RAY DIFFRACTION8chain 'C' and (resid 65 through 179 )
9X-RAY DIFFRACTION9chain 'C' and (resid 180 through 385 )
10X-RAY DIFFRACTION10chain 'C' and (resid 386 through 525 )
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 64 )
12X-RAY DIFFRACTION12chain 'D' and (resid 65 through 179 )
13X-RAY DIFFRACTION13chain 'D' and (resid 180 through 385 )
14X-RAY DIFFRACTION14chain 'D' and (resid 386 through 525 )
15X-RAY DIFFRACTION15chain 'E' and (resid 2 through 109 )
16X-RAY DIFFRACTION16chain 'E' and (resid 110 through 358 )
17X-RAY DIFFRACTION17chain 'E' and (resid 359 through 525 )
18X-RAY DIFFRACTION18chain 'F' and (resid 2 through 134 )
19X-RAY DIFFRACTION19chain 'F' and (resid 135 through 385 )
20X-RAY DIFFRACTION20chain 'F' and (resid 386 through 525 )
21X-RAY DIFFRACTION21chain 'G' and (resid 2 through 108 )
22X-RAY DIFFRACTION22chain 'G' and (resid 109 through 179 )
23X-RAY DIFFRACTION23chain 'G' and (resid 180 through 385 )
24X-RAY DIFFRACTION24chain 'G' and (resid 386 through 525 )
25X-RAY DIFFRACTION25chain 'H' and (resid 2 through 109 )
26X-RAY DIFFRACTION26chain 'H' and (resid 110 through 179 )
27X-RAY DIFFRACTION27chain 'H' and (resid 180 through 385 )
28X-RAY DIFFRACTION28chain 'H' and (resid 386 through 525 )
29X-RAY DIFFRACTION29chain 'I' and (resid 2 through 64 )
30X-RAY DIFFRACTION30chain 'I' and (resid 65 through 179 )
31X-RAY DIFFRACTION31chain 'I' and (resid 180 through 385 )
32X-RAY DIFFRACTION32chain 'I' and (resid 386 through 525 )
33X-RAY DIFFRACTION33chain 'J' and (resid 2 through 64 )
34X-RAY DIFFRACTION34chain 'J' and (resid 65 through 179 )
35X-RAY DIFFRACTION35chain 'J' and (resid 180 through 385 )
36X-RAY DIFFRACTION36chain 'J' and (resid 386 through 525 )
37X-RAY DIFFRACTION37chain 'K' and (resid 2 through 134 )
38X-RAY DIFFRACTION38chain 'K' and (resid 135 through 385 )
39X-RAY DIFFRACTION39chain 'K' and (resid 386 through 525 )
40X-RAY DIFFRACTION40chain 'L' and (resid 2 through 134 )
41X-RAY DIFFRACTION41chain 'L' and (resid 135 through 385 )
42X-RAY DIFFRACTION42chain 'L' and (resid 386 through 525 )
43X-RAY DIFFRACTION43chain 'M' and (resid 2 through 134 )
44X-RAY DIFFRACTION44chain 'M' and (resid 135 through 385 )
45X-RAY DIFFRACTION45chain 'M' and (resid 386 through 525 )
46X-RAY DIFFRACTION46chain 'N' and (resid 2 through 134 )
47X-RAY DIFFRACTION47chain 'N' and (resid 135 through 338 )
48X-RAY DIFFRACTION48chain 'N' and (resid 339 through 525 )

+
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