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- PDB-1ss8: GroEL -

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Basic information

Entry
Database: PDB / ID: 1ss8
TitleGroEL
ComponentsgroEL proteinGroEL
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 / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsChaudhry, C. / Horwich, A.L. / Brunger, A.T. / Adams, P.D.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states.
Authors: Chaudhry, C. / Horwich, A.L. / Brunger, A.T. / Adams, P.D.
History
DepositionMar 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 26, 2014Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE THE CONFLICTS ARE PRESENT IN RELATED ENTRY 1OEL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: groEL protein
B: groEL protein
C: groEL protein
D: groEL protein
E: groEL protein
F: groEL protein
G: groEL protein


Theoretical massNumber of molelcules
Total (without water)386,0367
Polymers386,0367
Non-polymers00
Water1,928107
1
A: groEL protein
B: groEL protein
C: groEL protein
D: groEL protein
E: groEL protein
F: groEL protein
G: groEL protein

A: groEL protein
B: groEL protein
C: groEL protein
D: groEL protein
E: groEL protein
F: groEL protein
G: groEL protein


Theoretical massNumber of molelcules
Total (without water)772,07214
Polymers772,07214
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area49340 Å2
ΔGint-218 kcal/mol
Surface area293910 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)178.380, 204.980, 280.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81A
91B
101C
111D
121E
131F
141G
12A
22B
32C
42D
52E
62F
72G
82A
92B
102C
112D
122E
132F
142G
13A
23B
33C
43D
53E
63F
73G

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALASERSERAA2 - 1351 - 134
211ALAALASERSERBB2 - 1351 - 134
311ALAALASERSERCC2 - 1351 - 134
411ALAALASERSERDD2 - 1351 - 134
511ALAALASERSEREE2 - 1351 - 134
611ALAALASERSERFF2 - 1351 - 134
711ALAALASERSERGG2 - 1351 - 134
821GLYGLYPROPROAA410 - 525409 - 524
921GLYGLYPROPROBB410 - 525409 - 524
1021GLYGLYPROPROCC410 - 525409 - 524
1121GLYGLYPROPRODD410 - 525409 - 524
1221GLYGLYPROPROEE410 - 525409 - 524
1321GLYGLYPROPROFF410 - 525409 - 524
1421GLYGLYPROPROGG410 - 525409 - 524
112VALVALVALVALAA136 - 190135 - 189
212VALVALVALVALBB136 - 190135 - 189
312VALVALVALVALCC136 - 190135 - 189
412VALVALVALVALDD136 - 190135 - 189
512VALVALVALVALEE136 - 190135 - 189
612VALVALVALVALFF136 - 190135 - 189
712VALVALVALVALGG136 - 190135 - 189
822GLYGLYGLUGLUAA375 - 409374 - 408
922GLYGLYGLUGLUBB375 - 409374 - 408
1022GLYGLYGLUGLUCC375 - 409374 - 408
1122GLYGLYGLUGLUDD375 - 409374 - 408
1222GLYGLYGLUGLUEE375 - 409374 - 408
1322GLYGLYGLUGLUFF375 - 409374 - 408
1422GLYGLYGLUGLUGG375 - 409374 - 408
113GLUGLUGLYGLYAA191 - 374190 - 373
213GLUGLUGLYGLYBB191 - 374190 - 373
313GLUGLUGLYGLYCC191 - 374190 - 373
413GLUGLUGLYGLYDD191 - 374190 - 373
513GLUGLUGLYGLYEE191 - 374190 - 373
613GLUGLUGLYGLYFF191 - 374190 - 373
713GLUGLUGLYGLYGG191 - 374190 - 373

NCS ensembles :
ID
1
2
3
DetailsTHE COMPLETE GROEL COMPLEX (2 BACK-TO-BACK RINGS) IS GENERATED BY THE APPLICATION OF THE SYMMETRY OPERATOR (X,-Y,-Z) TO THE 7 PROTOMERS IN THE ASYMMETRIC UNIT.

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Components

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


Mass: 55148.020 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: GROL, GROEL, MOPA, B4143, C5227, Z5748, ECS5124, SF4297, S4564
Plasmid: trc / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P0A6F5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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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: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 298 K / Method: evaporation, recrystallization / pH: 8
Details: PEG 8000, 1.72 M ammonium slufate, 4 mM CaCl2, 100mM Tris-acetate , pH 8.0, EVAPORATION, RECRYSTALLIZATION, temperature 298K

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→30.015 Å / Num. all: 123506 / Num. obs: 117825 / Limit h max: 60 / Limit h min: 0 / Limit k max: 75 / Limit k min: 0 / Limit l max: 100 / Limit l min: 0

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.89 / SU B: 14.259 / SU ML: 0.279 / SU R Cruickshank DPI: 1.208 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 1.208 / ESU R Free: 0.334 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2966 2.517 %RANDOM
Rwork0.215 ---
all0.216 117825 --
obs0.216 117825 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 2.604 Å2
Baniso -1Baniso -2Baniso -3
1--1.211 Å20 Å20 Å2
2---1.539 Å20 Å2
3---2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26957 0 0 107 27064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.02227153
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.98436666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88153661
X-RAY DIFFRACTIONr_chiral_restr0.1340.24466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219740
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2652
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4220.298
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3670.25
X-RAY DIFFRACTIONr_mcbond_it0.2971.518081
X-RAY DIFFRACTIONr_mcangle_it0.489228938
X-RAY DIFFRACTIONr_scbond_it1.13739072
X-RAY DIFFRACTIONr_scangle_it1.5624.57728
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1806tight positional0.0920.05
11A1806tight thermal0.1920.5
12B1806tight positional0.1310.05
12B1806tight thermal0.2280.5
13C1806tight positional0.0980.05
13C1806tight thermal0.1890.5
14D1806tight positional0.0870.05
14D1806tight thermal0.190.5
15E1806tight positional0.1080.05
15E1806tight thermal0.2160.5
16F1806tight positional0.0910.05
16F1806tight thermal0.1820.5
17G1806tight positional0.0920.05
17G1806tight thermal0.1930.5
21A647tight positional0.0720.05
21A647tight thermal0.1090.5
22B647tight positional0.0760.05
22B647tight thermal0.1310.5
23C647tight positional0.0730.05
23C647tight thermal0.1050.5
24D647tight positional0.070.05
24D647tight thermal0.1080.5
25E647tight positional0.0830.05
25E647tight thermal0.1320.5
26F647tight positional0.0710.05
26F647tight thermal0.1020.5
27G647tight positional0.0760.05
27G647tight thermal0.1340.5
31A1398tight positional0.0510.05
31A1398tight thermal0.0740.5
32B1398tight positional0.0490.05
32B1398tight thermal0.0620.5
33C1398tight positional0.0530.05
33C1398tight thermal0.0680.5
34D1398tight positional0.0520.05
34D1398tight thermal0.0710.5
35E1398tight positional0.0620.05
35E1398tight thermal0.0840.5
36F1398tight positional0.0430.05
36F1398tight thermal0.0550.5
37G1398tight positional0.0530.05
37G1398tight thermal0.0710.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection all
2.7-2.76960.3681040.3274270X-RAY DIFFRACTION5287
2.77-2.84480.3451360.2955988X-RAY DIFFRACTION6982
2.845-2.92650.3051850.2847102X-RAY DIFFRACTION8113
2.927-3.01570.2971800.2637032X-RAY DIFFRACTION7907
3.016-3.11350.2751680.2467055X-RAY DIFFRACTION7730
3.114-3.22160.2911770.2316979X-RAY DIFFRACTION7520
3.222-3.34170.2521890.227037X-RAY DIFFRACTION7486
3.342-3.47640.2731860.2236976X-RAY DIFFRACTION7427
3.476-3.62870.2361910.2136994X-RAY DIFFRACTION7417
3.629-3.80310.251710.2076983X-RAY DIFFRACTION7317
3.803-4.00520.221990.1976673X-RAY DIFFRACTION7046
4.005-4.24340.2341590.1846519X-RAY DIFFRACTION6776
4.243-4.530.221350.1796199X-RAY DIFFRACTION6395
4.53-4.88360.241550.1895753X-RAY DIFFRACTION5977
4.884-5.33560.2361550.2035329X-RAY DIFFRACTION5543
5.336-5.9420.3021360.2324915X-RAY DIFFRACTION5098
5.942-6.81680.2821170.244365X-RAY DIFFRACTION4527
6.817-8.24310.193870.1873755X-RAY DIFFRACTION3866
8.243-11.24090.149840.153012X-RAY DIFFRACTION3109
11.241-300.264520.291923X-RAY DIFFRACTION1983
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)
11.7331-0.56150.16772.42240.04991.0618-0.06920.09730.0207-0.06080.0442-0.1251-0.06030.21990.0250.1395-0.02140.03010.15020.03410.06811.8149.025-16.046
20.7464-0.40060.50774.32882.40910.4065-0.05580.2315-0.3382-0.08920.5362-0.6425-1.1021.2376-0.48040.4720.04280.11580.68230.01520.285421.1468.094-29.449
38.3958-0.8165-0.23938.5617-0.57636.79740.3758-0.0226-0.6832-0.3895-0.635-0.61710.7931.0920.25920.95340.37040.02850.8082-0.03470.383311.1288.198-53.402
42.7420.21050.33141.39340.04090.6243-0.030.0144-0.0111-0.00670.03150.0637-0.093-0.0192-0.00150.1391-0.0122-0.00490.09150.05030.0616-22.27241.447-15.065
55.3541-3.5657-3.22855.01556.2018.96040.14630.00240.8154-0.30710.16-1.0675-0.16920.3375-0.30620.2792-0.1433-0.02840.30090.04890.366-9.50956.31-28.196
610.56690.45920.32267.5238-0.34376.35430.26571.33820.0652-0.1697-0.1015-0.349-0.3671.3108-0.16410.55690.07450.00731.33160.11890.417-14.59847.938-52.319
72.59440.4703-0.14252.31960.19250.9280.03230.05810.17320.0272-0.0124-0.0421-0.136-0.0161-0.01990.11880.0221-0.01850.13270.05590.0605-62.23842.918-15.384
84.56580.6516-4.0187-1.30571.110810.29980.64770.37290.679-0.5587-0.4004-1.0534-0.4594-1.0335-0.24730.3958-0.0674-0.1390.38750.13210.2403-65.57562.241-28.515
911.06330.66530.7588.42590.28034.9666-0.24520.4625-0.0936-0.17590.1082-0.8788-0.66780.64490.1370.6168-0.08150.09890.76940.02540.5619-61.72153.137-53.043
101.8004-0.1017-0.11353.34810.12130.63390.03640.13440.03040.04620.00110.237-0.0191-0.1455-0.03750.141-0.0203-0.01790.15250.02970.0479-88.46612.544-16.135
112.24872.3861-2.45075.0534-3.11169.49530.35010.33980.86460.01450.28620.36070.6153-1.0063-0.63630.5750.0826-0.12120.47510.00750.3116-105.23922.323-29.363
128.9987-1.25010.22659.41630.52636.13860.182-0.2161.3883-0.6242-0.21870.0693-1.1584-0.74030.03671.15210.12740.07140.57290.00990.4918-96.22919.421-53.779
132.1305-0.1192-0.02141.7722-0.17320.733-0.01160.07020.0376-0.08430.0622-0.0330.0343-0.034-0.05060.1195-0.0382-0.02410.1026-0.00850.0078-81.008-26.959-17.064
141.1355-1.1067-0.71384.9389-4.15117.5659-0.29830.1491-0.0376-0.41860.4710.73860.4195-0.1011-0.17270.1454-0.0053-0.02830.4252-0.01350.216-99.023-33.636-30.526
158.9994-0.9388-0.07348.13680.48865.7087-0.1009-0.0395-0.05650.15140.03070.5897-0.1158-0.97940.07020.4935-0.0014-0.05990.80890.0680.2185-90.049-27.807-54.254
163.10870.367-0.03922.0373-0.31310.84320.05850.0136-0.2883-0.0942-0.0335-0.01170.2556-0.029-0.0250.19570.0032-0.0180.1553-0.04220.1122-45.577-45.929-17.7
176.9522-1.17744.78345.674-2.9148.31630.45020.3181-1.57020.24480.2089-0.07750.75760.0601-0.65910.6178-0.05-0.09350.382-0.19290.6987-50.935-64.265-31.611
1813.81051.0874-0.36488.45670.19555.9333-0.5372.379-0.042-0.46130.38950.5450.743-0.93670.14740.6971-0.2739-0.02271.5948-0.09360.6169-49.857-53.188-55.401
191.6590.2269-0.14983.1429-0.00271.0260.0330.0652-0.04320.0625-0.0345-0.09960.09760.0990.00150.13120.03210.01440.12120.00970.0367-8.846-29.691-17.378
204.42861.52713.89092.8705-0.356610.59750.45990.4515-0.80420.5204-0.2493-0.2854-0.01451.1833-0.21060.59170.03170.04330.4012-0.01740.31962.186-44.95-31.444
218.5195-0.113-0.81399.072-0.22586.217-0.1694-0.3833-0.254-0.37820.01910.60580.9342-0.12260.15030.7798-0.0378-0.00810.5555-0.00550.3246-5.496-36.69-55.117
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 1351 - 134
21AA410 - 525409 - 524
32AA136 - 190135 - 189
42AA375 - 409374 - 408
53AA191 - 374190 - 373
64BB2 - 1351 - 134
74BB410 - 525409 - 524
85BB136 - 190135 - 189
95BB375 - 409374 - 408
106BB191 - 374190 - 373
117CC2 - 1351 - 134
127CC410 - 525409 - 524
138CC136 - 190135 - 189
148CC375 - 409374 - 408
159CC191 - 374190 - 373
1610DD2 - 1351 - 134
1710DD410 - 525409 - 524
1811DD136 - 190135 - 189
1911DD375 - 409374 - 408
2012DD191 - 374190 - 373
2113EE2 - 1351 - 134
2213EE410 - 525409 - 524
2314EE136 - 190135 - 189
2414EE375 - 409374 - 408
2515EE191 - 374190 - 373
2616FF2 - 1351 - 134
2716FF410 - 525409 - 524
2817FF136 - 190135 - 189
2917FF375 - 409374 - 408
3018FF191 - 374190 - 373
3119GG2 - 1351 - 134
3219GG410 - 525409 - 524
3320GG136 - 190135 - 189
3420GG375 - 409374 - 408
3521GG191 - 374190 - 373

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