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- PDB-1oel: CONFORMATIONAL VARIABILITY IN THE REFINED STRUCTURE OF THE CHAPER... -

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Basic information

Entry
Database: PDB / ID: 1oel
TitleCONFORMATIONAL VARIABILITY IN THE REFINED STRUCTURE OF THE CHAPERONIN GROEL AT 2.8 ANGSTROM RESOLUTION
ComponentsGROEL (HSP60 CLASS)
KeywordsCHAPERONIN
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / : / 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 / : / 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 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate 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 / Resolution: 2.8 Å
AuthorsBraig, K. / Adams, P.D. / Brunger, A.T.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution.
Authors: Braig, K. / Adams, P.D. / Brunger, A.T.
#1: Journal: Nature / Year: 1994
Title: The Crystal Structure of the Bacterial Chaperonin Groel at 2.8 Angstrom
Authors: Braig, K. / Otwinowski, Z. / Hegde, R. / Boisvert, D.C. / Joachimiak, A. / Horwich, A.L. / Sigler, P.B.
#2: Journal: Nature / Year: 1994
Title: Residues in Chaperonin Groel Required for Polypeptide Binding and Release
Authors: Fenton, W.A. / Kashi, Y. / Furtak, K. / Horwich, A.L.
History
DepositionNov 21, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GROEL (HSP60 CLASS)
B: GROEL (HSP60 CLASS)
C: GROEL (HSP60 CLASS)
D: GROEL (HSP60 CLASS)
E: GROEL (HSP60 CLASS)
F: GROEL (HSP60 CLASS)
G: GROEL (HSP60 CLASS)


Theoretical massNumber of molelcules
Total (without water)399,8987
Polymers399,8987
Non-polymers00
Water2,684149
1
A: GROEL (HSP60 CLASS)
B: GROEL (HSP60 CLASS)
C: GROEL (HSP60 CLASS)
D: GROEL (HSP60 CLASS)
E: GROEL (HSP60 CLASS)
F: GROEL (HSP60 CLASS)
G: GROEL (HSP60 CLASS)

A: GROEL (HSP60 CLASS)
B: GROEL (HSP60 CLASS)
C: GROEL (HSP60 CLASS)
D: GROEL (HSP60 CLASS)
E: GROEL (HSP60 CLASS)
F: GROEL (HSP60 CLASS)
G: GROEL (HSP60 CLASS)


Theoretical massNumber of molelcules
Total (without water)799,79614
Polymers799,79614
Non-polymers00
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
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

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Components

#1: Protein
GROEL (HSP60 CLASS)


Mass: 57128.293 Da / Num. of mol.: 7 / Mutation: R13G, A126V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Description: OVER-EXPRESSION PLASMID / Gene: GROEL / Plasmid: IQ-TRC / Gene (production host): GROEL / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal grow
*PLUS
Temperature: 28 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlGroEL1drop
20.2 %(w/v)PEG80001drop
30.86 Mammonium sulfate1drop
42 mM1dropCaCl2
550 mMTris-acetate1drop
60.4 %(w/v)PEG80001reservoir
74 mM1reservoirCaCl2
8100 mMTris-acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→8.01 Å / Num. obs: 117943 / % possible obs: 88.2 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementResolution: 2.8→6 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.27 -10 %
Rwork0.227 --
obs0.227 90526 72.2 %
Displacement parametersBiso mean: 51.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26936 0 0 149 27085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.301
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.301
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.89 Å / Rfactor Rfree: 32.2 / Total num. of bins used: 10 / Rfactor obs: 28.9

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