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- PDB-1kid: GROEL (HSP60 CLASS) FRAGMENT (APICAL DOMAIN) COMPRISING RESIDUES ... -

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Basic information

Entry
Database: PDB / ID: 1kid
TitleGROEL (HSP60 CLASS) FRAGMENT (APICAL DOMAIN) COMPRISING RESIDUES 191-376, MUTANT WITH ALA 262 REPLACED WITH LEU AND ILE 267 REPLACED WITH MET
ComponentsGROEL (HSP60 CLASS)
KeywordsCHAPERONE / HSP60 / GROEL / CELL DIVISION / ATP-BINDING / PHOSPHORYLATION
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 / 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: 1.7 Å
AuthorsBuckle, A.M. / Fersht, A.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: A structural model for GroEL-polypeptide recognition.
Authors: Buckle, A.M. / Zahn, R. / Fersht, A.R.
History
DepositionDec 13, 1996Processing site: BNL
Revision 1.0Sep 17, 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: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)22,0601
Polymers22,0601
Non-polymers00
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.720, 63.810, 75.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsRESIDUES 184 - 190 (PART OF A FUSED N-TERMINAL TAG) BINDS IN THE PUTATIVE POLYPEPTIDE-BINDING SITE OF A NEIGHBORING MOLECULE IN THE CRYSTAL LATTICE. THIS "MINI-CHAPERONE - PEPTIDE COMPLEX" CAN BE GENERATED BY APPLYING THE TRANSFORMATION 1/2 - X, -Y, 1/2+Z TO THE N-TERMINAL TAG (RESIDUES 184 - 190) AND COMBINING THE RESULTING COORDINATES WITH RESIDUES.

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Components

#1: Protein GROEL (HSP60 CLASS) / 60 KD CHAPERONIN / PROTEIN CPN60


Mass: 22060.316 Da / Num. of mol.: 1 / Fragment: APICAL DOMAIN, RESIDUES 191 - 376 / Mutation: A262L, I267M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Cellular location: CYTOPLASM / Plasmid: PRSET (INVITROGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.6 Å3/Da / Density % sol: 52.52 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlprotein1drop
20.5 M1dropNaCl
350 mMTris-HCl1drop
425 %glycerol1drop
51.0 M1reservoirNaCl
6100 mMTris-HCl1reservoir
725 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.7→12.8 Å / Num. obs: 25290 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 4.9 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.2 / % possible all: 85.6
Reflection
*PLUS
Num. measured all: 260633
Reflection shell
*PLUS
% possible obs: 85.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RESIDUES 191 - 345 OF PDB ENTRY 1JON

1jon


Resolution: 1.7→12.8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.224 2443 10 %
Rwork0.18 --
obs-25290 97.6 %
Displacement parametersBiso mean: 17.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→12.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 0 292 1746
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4352
X-RAY DIFFRACTIONp_mcangle_it1.9613
X-RAY DIFFRACTIONp_scbond_it2.3092
X-RAY DIFFRACTIONp_scangle_it3.4985
X-RAY DIFFRACTIONp_plane_restr0.02470.03
X-RAY DIFFRACTIONp_chiral_restr0.1440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.2690.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1850.3
X-RAY DIFFRACTIONp_planar_tor4.215
X-RAY DIFFRACTIONp_staggered_tor15.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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