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- PDB-1jon: GROEL (HSP60 CLASS) FRAGMENT COMPRISING RESIDUES 191-345 -

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Basic information

Entry
Database: PDB / ID: 1jon
TitleGROEL (HSP60 CLASS) FRAGMENT COMPRISING RESIDUES 191-345
ComponentsGROEL, HSP60 CLASS
KeywordsCHAPERONE / CELL DIVISION / ATP-BINDING / PHOSPHORYLATION
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 / 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 ...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 / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBuckle, A.M. / Fersht, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Chaperone activity and structure of monomeric polypeptide binding domains of GroEL.
Authors: Zahn, R. / Buckle, A.M. / Perrett, S. / Johnson, C.M. / Corrales, F.J. / Golbik, R. / Fersht, A.R.
History
DepositionMay 30, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 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


Theoretical massNumber of molelcules
Total (without water)16,6421
Polymers16,6421
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.670, 91.670, 38.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein GROEL, HSP60 CLASS


Mass: 16642.238 Da / Num. of mol.: 1
Fragment: POLYPEPTIDE BINDING (APICAL) DOMAIN, RESIDUES 191 - 345
Mutation: A262L, I267M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Organ: TAIL / Plasmid: PRSET (INVITROGEN)
Gene (production host): GROEL FRAGMENT COMPRISING RESIDUES 191 - 345
Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / pH: 8.5
Details: 11% PEG 4000, 50 MM TRIS-HCL, PH 8.5, 200 MM LISO4, 23 MG/ML PROTEIN, 17 DEG. C., temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlprotein1drop
211 %PEG40001drop
350 mMTris-HCl1drop
4100 mM1dropLi2SO4
522 %PEG40001reservoir
6100 mMTris-HCl1reservoir
7200 mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 9, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→22 Å / Num. obs: 6564 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.8 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 21762
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameClassification
AMoREphasing
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEL

1oel


Resolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.287 -10 %
Rwork0.216 --
obs0.216 6341 99.5 %
Displacement parametersBiso mean: 42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1026 0 0 8 1034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.423
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.214 / Rfactor Rfree: 0.291
Solvent computation
*PLUS
Displacement parameters
*PLUS

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