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- PDB-4wsc: Crystal structure of a GroELK105A mutant -

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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 / identical protein binding / membrane / 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

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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)802,67114
Polymers802,67114
Non-polymers00
Water00
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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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: 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

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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 )

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