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- PDB-1dkd: CRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A DODECAMERIC PE... -

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Basic information

Entry
Database: PDB / ID: 1dkd
TitleCRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A DODECAMERIC PEPTIDE COMPLEX
Components
  • 12-MER PEPTIDE
  • GROEL
KeywordsCHAPERONE / MOLECULAR CHAPERON / HSP60 / PROTEIN FOLDING / PEPTIDE SELECTION / PHAGE DISPLAY / PEPTIDE BINDING GROOVE FORMED BY PAIRED HELICES SUBSTRATE PEPTIDE IN BETA-SHEET
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 / Resolution: 2.1 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 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 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

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Assembly

Deposited unit
A: GROEL
E: 12-MER PEPTIDE
B: GROEL
F: 12-MER PEPTIDE
C: GROEL
G: 12-MER PEPTIDE
D: GROEL
H: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)68,7608
Polymers68,7608
Non-polymers00
Water1,72996
1
A: GROEL
E: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area7400 Å2
MethodPISA
2
B: GROEL
F: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area7450 Å2
MethodPISA
3
C: GROEL
G: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-7 kcal/mol
Surface area7590 Å2
MethodPISA
4
D: GROEL
H: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area7630 Å2
MethodPISA
5
A: GROEL
E: 12-MER PEPTIDE
C: GROEL
G: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)34,3804
Polymers34,3804
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-27 kcal/mol
Surface area13550 Å2
MethodPISA
6
B: GROEL
F: 12-MER PEPTIDE

D: GROEL
H: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)34,3804
Polymers34,3804
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area3260 Å2
ΔGint-27 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.042, 134.668, 59.734
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GROEL / CHAPERONE HSP60


Mass: 15729.269 Da / Num. of mol.: 4 / 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: Protein/peptide
12-MER PEPTIDE


Mass: 1460.676 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: the peptide was chemically synthesized and was SELECTED FROM PHAGE DISPLAY PEPTIDE LIBRARY.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe peptide adopts a typical beta-turn; paired alpha helices H and I, and the groove between them ...The peptide adopts a typical beta-turn; paired alpha helices H and I, and the groove between them constitute the binding site.

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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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4K, MgCl2, TrisCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-Cl1reservoir
2200 mM1reservoirMgCl2
330 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.923
DetectorType: BRANDEIS / Detector: CCD / Date: Sep 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.923 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 38529 / Num. obs: 35897 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.303 / Num. unique all: 3394 / % possible all: 89.9
Reflection shell
*PLUS
% possible obs: 89.9 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.1→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1783 -random
Rwork0.215 ---
all-38529 --
obs-35897 93.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 0 96 4818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_bond_d0.007
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6

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