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- PDB-1dk7: CRYSTAL STRUCTURE OF AN ISOLATED APICAL DOMAIN OF GROEL -

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Basic information

Entry
Database: PDB / ID: 1dk7
TitleCRYSTAL STRUCTURE OF AN ISOLATED APICAL DOMAIN OF GROEL
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 / Resolution: 2.02 Å
AuthorsChen, L. / Sigler, P.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity.
Authors: Chen, L. / Sigler, P.B.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROEL
B: GROEL


Theoretical massNumber of molelcules
Total (without water)31,4592
Polymers31,4592
Non-polymers00
Water3,387188
1
A: GROEL


Theoretical massNumber of molelcules
Total (without water)15,7291
Polymers15,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GROEL


Theoretical massNumber of molelcules
Total (without water)15,7291
Polymers15,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.859, 84.859, 77.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GROEL / / CHAPERONE HSP60


Mass: 15729.269 Da / Num. of mol.: 2 / Fragment: APICAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 292.3 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4K, LI2SO4, TRISHCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 19.3K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
2100 mMTris/Cl1reservoir
3200 mM1reservoirLi2SO4
430 %PEG40001reservoir
1apocal domain1drop1:1(v/v) ratio of 10 mg/ml of the apical domain to well solution

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: BRANDEIS / Detector: CCD / Date: Nov 29, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 22062 / Num. obs: 18450 / % possible obs: 83.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.327 / Num. unique all: 2038 / % possible all: 96.9
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.02→15.15 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 542879.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1815 9.8 %RANDOM
Rwork0.225 ---
obs0.225 18450 86.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.36 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-4.94 Å24.4 Å20 Å2
2--4.94 Å20 Å2
3----9.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.02→15.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 0 188 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.621.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it4.032.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.277 259 9.7 %
Rwork0.257 2409 -
obs--73.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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