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- PDB-1la1: Gro-EL Fragment (Apical Domain) Comprising Residues 188-379 -

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Basic information

Entry
Database: PDB / ID: 1la1
TitleGro-EL Fragment (Apical Domain) Comprising Residues 188-379
ComponentsGroEL
KeywordsCHAPERONE / MOLECULAR CHAPERONE / 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 / 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: 2.06 Å
AuthorsAshcroft, A.E. / Brinker, A. / Coyle, J.E. / Weber, F. / Kaiser, M. / Moroder, L. / Parsons, M.R. / Jager, J. / Hartl, U.F. / Hayer-Hartl, M. / Radford, S.E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural plasticity and noncovalent substrate binding in the GroEL apical domain. A study using electrospay ionization mass spectrometry and fluorescence binding studies.
Authors: Ashcroft, A.E. / Brinker, A. / Coyle, J.E. / Weber, F. / Kaiser, M. / Moroder, L. / Parsons, M.R. / Jager, J. / Hartl, U.F. / Hayer-Hartl, M. / Radford, S.E.
History
DepositionMar 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GroEL


Theoretical massNumber of molelcules
Total (without water)20,7281
Polymers20,7281
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.620, 61.950, 75.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GroEL / / chaperone Hsp60 / peptide-dependent ATPase / heat shock protein


Mass: 20727.852 Da / Num. of mol.: 1 / Fragment: Apical Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.6 M NaCl, 14 % (w/v) PEG 6000, 100 mM Tris/HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1drop
21 mMdithiothreitol1droppH7.2
310 mg/mlprotein1drop
40.6 M1reservoirNaCl
514 %(w/v)PEG60001reservoir
6100 mMTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 1999 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. all: 15933 / Num. obs: 14319 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Biso Wilson estimate: 18.4 Å2 / Net I/σ(I): 10.1
Reflection
*PLUS
Rmerge(I) obs: 0.387

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apical domain derived from 1OEL

1oel


Resolution: 2.06→19.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1242127.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: CNS 1.0 followed by REFMAC was used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1401 9.8 %RANDOM
Rwork0.197 ---
all-15933 --
obs-14319 98.2 %-
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2--4.05 Å20 Å2
3----6.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.06→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 0 274 1722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d2.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d3.03
LS refinement shellResolution: 2.06→2.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2842 199 8.7 %
Rwork0.2491 2082 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Rfactor obs: 0.197 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.03
LS refinement shell
*PLUS
Rfactor Rfree: 0.2842 / Rfactor Rwork: 0.2491 / Rfactor obs: 0.2491

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