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- PDB-2nwc: A 3.02 angstrom crystal structure of wild-type apo GroEL in a mon... -

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Basic information

Entry
Database: PDB / ID: 2nwc
TitleA 3.02 angstrom crystal structure of wild-type apo GroEL in a monoclinic space group
Components60 kDa chaperonin
KeywordsCHAPERONE / chaperonin / HSP60
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 / cytoplasm
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
Chaperonin GroEL / Chaperonin GroEL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsKiser, P.D. / Lodowski, D.T. / Palczewski, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Purification, crystallization and structure determination of native GroEL from Escherichia coli lacking bound potassium ions
Authors: Kiser, P.D. / Lodowski, D.T. / Palczewski, K.
History
DepositionNov 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)801,64714
Polymers801,64714
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51440 Å2
ΔGint-218 kcal/mol
Surface area290000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.423, 262.254, 147.074
Angle α, β, γ (deg.)90.00, 99.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C
51E
61F
71G
81D
91A
101B
111C
121E
131F
141G
151D
161A
171B
181C
191E
201F
211G
221D
231A
241B
251C
261E
271F
281G
291D
301A
311B
321C
331E
341F
351G
361D
371A
381B
391C
401E
411F
421G
12H
22N
32I
42J
52L
62M
72K
82H
92N
102I
112J
122L
132M
142K
152H
162N
172I
182J
192L
202M
212K
222H
232N
242I
252J
262L
272M
282K
292H
302N
312I
322J
332L
342M
352K
362H
372N
382I
392J
402L
412M
422K

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAVALVAL1DD2 - 391 - 38
211ALAALAVALVAL1AA2 - 391 - 38
311ALAALAVALVAL1BB2 - 391 - 38
411ALAALAVALVAL1CC2 - 391 - 38
511ALAALAVALVAL1EE2 - 391 - 38
611ALAALAVALVAL1FF2 - 391 - 38
711ALAALAVALVAL1GG2 - 391 - 38
821LEULEUALAALA6DD40 - 4639 - 45
921LEULEUALAALA6AA40 - 4639 - 45
1021LEULEUALAALA6BB40 - 4639 - 45
1121LEULEUALAALA6CC40 - 4639 - 45
1221LEULEUALAALA6EE40 - 4639 - 45
1321LEULEUALAALA6FF40 - 4639 - 45
1421LEULEUALAALA6GG40 - 4639 - 45
1531PROPROPHEPHE1DD47 - 19546 - 194
1631PROPROPHEPHE1AA47 - 19546 - 194
1731PROPROPHEPHE1BB47 - 19546 - 194
1831PROPROPHEPHE1CC47 - 19546 - 194
1931PROPROPHEPHE1EE47 - 19546 - 194
2031PROPROPHEPHE1FF47 - 19546 - 194
2131PROPROPHEPHE1GG47 - 19546 - 194
2241ASPASPASPASP6DD196 - 224195 - 223
2341ASPASPASPASP6AA196 - 224195 - 223
2441ASPASPASPASP6BB196 - 224195 - 223
2541ASPASPASPASP6CC196 - 224195 - 223
2641ASPASPASPASP6EE196 - 224195 - 223
2741ASPASPASPASP6FF196 - 224195 - 223
2841ASPASPASPASP6GG196 - 224195 - 223
2951LYSLYSASPASP6DD225 - 473224 - 472
3051LYSLYSASPASP6AA225 - 473224 - 472
3151LYSLYSASPASP6BB225 - 473224 - 472
3251LYSLYSASPASP6CC225 - 473224 - 472
3351LYSLYSASPASP6EE225 - 473224 - 472
3451LYSLYSASPASP6FF225 - 473224 - 472
3551LYSLYSASPASP6GG225 - 473224 - 472
3661ILEILEPROPRO1DD489 - 525488 - 524
3761ILEILEPROPRO1AA489 - 525488 - 524
3861ILEILEPROPRO1BB489 - 525488 - 524
3961ILEILEPROPRO1CC489 - 525488 - 524
4061ILEILEPROPRO1EE489 - 525488 - 524
4161ILEILEPROPRO1FF489 - 525488 - 524
4261ILEILEPROPRO1GG489 - 525488 - 524
112ALAALAVALVAL1HH2 - 391 - 38
212ALAALAVALVAL1NN2 - 391 - 38
312ALAALAVALVAL1II2 - 391 - 38
412ALAALAVALVAL1JJ2 - 391 - 38
512ALAALAVALVAL1LL2 - 391 - 38
612ALAALAVALVAL1MM2 - 391 - 38
712ALAALAVALVAL1KK2 - 391 - 38
822LEULEUALAALA6HH40 - 4639 - 45
922LEULEUALAALA6NN40 - 4639 - 45
1022LEULEUALAALA6II40 - 4639 - 45
1122LEULEUALAALA6JJ40 - 4639 - 45
1222LEULEUALAALA6LL40 - 4639 - 45
1322LEULEUALAALA6MM40 - 4639 - 45
1422LEULEUALAALA6KK40 - 4639 - 45
1532PROPROPHEPHE1HH47 - 19546 - 194
1632PROPROPHEPHE1NN47 - 19546 - 194
1732PROPROPHEPHE1II47 - 19546 - 194
1832PROPROPHEPHE1JJ47 - 19546 - 194
1932PROPROPHEPHE1LL47 - 19546 - 194
2032PROPROPHEPHE1MM47 - 19546 - 194
2132PROPROPHEPHE1KK47 - 19546 - 194
2242ASPASPASPASP6HH196 - 224195 - 223
2342ASPASPASPASP6NN196 - 224195 - 223
2442ASPASPASPASP6II196 - 224195 - 223
2542ASPASPASPASP6JJ196 - 224195 - 223
2642ASPASPASPASP6LL196 - 224195 - 223
2742ASPASPASPASP6MM196 - 224195 - 223
2842ASPASPASPASP6KK196 - 224195 - 223
2952LYSLYSASPASP6HH225 - 473224 - 472
3052LYSLYSASPASP6NN225 - 473224 - 472
3152LYSLYSASPASP6II225 - 473224 - 472
3252LYSLYSASPASP6JJ225 - 473224 - 472
3352LYSLYSASPASP6LL225 - 473224 - 472
3452LYSLYSASPASP6MM225 - 473224 - 472
3552LYSLYSASPASP6KK225 - 473224 - 472
3662ILEILEPROPRO1HH489 - 525488 - 524
3762ILEILEPROPRO1NN489 - 525488 - 524
3862ILEILEPROPRO1II489 - 525488 - 524
3962ILEILEPROPRO1JJ489 - 525488 - 524
4062ILEILEPROPRO1LL489 - 525488 - 524
4162ILEILEPROPRO1MM489 - 525488 - 524
4262ILEILEPROPRO1KK489 - 525488 - 524

NCS ensembles :
ID
1
2
DetailsBiological assembly is identical to that of deposited coordinates.

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Components

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


Mass: 57260.504 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: groL, groEL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2(DE3)pLysS
References: UniProt: Q1R3B6, UniProt: P0A6F5*PLUS, EC: 3.6.4.9

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 0.1 M imidazole, 35% MPD, 0.2 M MgCl2, pH 8.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.02→50 Å / Num. all: 202060 / Num. obs: 202060 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rsym value: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 3.02→3.13 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.02 / Num. unique all: 20078 / Rsym value: 0.757 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1kp8
Resolution: 3.02→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 44.905 / SU ML: 0.358 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26269 10042 5.1 %RANDOM
Rwork0.2266 ---
obs0.22841 188012 99.72 %-
all-198054 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.399 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å22.6 Å2
2---3.3 Å20 Å2
3---5.65 Å2
Refinement stepCycle: LAST / Resolution: 3.02→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53970 0 0 0 53970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02254362
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.98873402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.47957322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5226.0672100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4611510080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.94115308
X-RAY DIFFRACTIONr_chiral_restr0.0660.28932
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0239494
X-RAY DIFFRACTIONr_nbd_refined0.1840.225139
X-RAY DIFFRACTIONr_nbtor_refined0.2880.238349
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.21284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.26
X-RAY DIFFRACTIONr_mcbond_it0.1941.537177
X-RAY DIFFRACTIONr_mcangle_it0.326257876
X-RAY DIFFRACTIONr_scbond_it0.411318651
X-RAY DIFFRACTIONr_scangle_it0.7334.515526
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11D1619tight positional0.010.05
12A1619tight positional0.020.05
13B1619tight positional0.010.05
14C1619tight positional0.010.05
15E1619tight positional0.010.05
16F1619tight positional0.010.05
17G1619tight positional0.030.05
21H1619tight positional0.010.05
22N1619tight positional0.010.05
23I1619tight positional0.010.05
24J1619tight positional0.010.05
25L1619tight positional0.010.05
26M1619tight positional0.010.05
27K1619tight positional0.010.05
11D2121loose positional0.475
12A2121loose positional1.375
13B2121loose positional1.265
14C2121loose positional0.765
15E2121loose positional0.785
16F2121loose positional0.545
17G2121loose positional0.545
21H2121loose positional0.625
22N2121loose positional0.475
23I2121loose positional0.645
24J2121loose positional0.65
25L2121loose positional0.915
26M2121loose positional0.815
27K2121loose positional0.645
11D1619tight thermal0.020.5
12A1619tight thermal0.020.5
13B1619tight thermal0.020.5
14C1619tight thermal0.020.5
15E1619tight thermal0.020.5
16F1619tight thermal0.020.5
17G1619tight thermal0.020.5
21H1619tight thermal0.020.5
22N1619tight thermal0.020.5
23I1619tight thermal0.020.5
24J1619tight thermal0.020.5
25L1619tight thermal0.020.5
26M1619tight thermal0.020.5
27K1619tight thermal0.020.5
11D2121loose thermal0.8210
12A2121loose thermal0.710
13B2121loose thermal0.6710
14C2121loose thermal0.6510
15E2121loose thermal0.6110
16F2121loose thermal0.7110
17G2121loose thermal0.7310
21H2121loose thermal0.6110
22N2121loose thermal0.8410
23I2121loose thermal0.6410
24J2121loose thermal0.6610
25L2121loose thermal0.6410
26M2121loose thermal0.5910
27K2121loose thermal0.6510
LS refinement shellResolution: 3.02→3.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 758 -
Rwork0.348 13658 -
obs--98.92 %

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