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- PDB-1grl: THE CRYSTAL STRUCTURE OF THE BACTERIAL CHAPERONIN GROEL AT 2.8 AN... -

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Basic information

Entry
Database: PDB / ID: 1grl
TitleTHE CRYSTAL STRUCTURE OF THE BACTERIAL CHAPERONIN GROEL AT 2.8 ANGSTROMS
ComponentsGROEL (HSP60 CLASS)
KeywordsCHAPERONIN
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 / cytoplasm
Similarity search - Function
GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily ...GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GROEL; domain 1 / GroEL-like equatorial domain / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chaperonin GroEL / Chaperonin GroEL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBraig, K. / Otwinowski, Z. / Hegde, R. / Boisvert, D.C. / Joachimiak, A. / Horwich, A.L. / Sigler, P.B.
Citation
Journal: Nature / Year: 1994
Title: The crystal structure of the bacterial chaperonin GroEL at 2.8 A.
Authors: K Braig / Z Otwinowski / R Hegde / D C Boisvert / A Joachimiak / A L Horwich / P B Sigler /
Abstract: The crystal structure of Escherichia coli GroEL shows a porous cylinder of 14 subunits made of two nearly 7-fold rotationally symmetrical rings stacked back-to-back with dyad symmetry. The subunits ...The crystal structure of Escherichia coli GroEL shows a porous cylinder of 14 subunits made of two nearly 7-fold rotationally symmetrical rings stacked back-to-back with dyad symmetry. The subunits consist of three domains: a large equatorial domain that forms the foundation of the assembly at its waist and holds the rings together; a large loosely structured apical domain that forms the ends of the cylinder; and a small slender intermediate domain that connects the two, creating side windows. The three-dimensional structure places most of the mutationally defined functional sites on the channel walls and its outward invaginations, and at the ends of the cylinder.
#1: Journal: Nature / Year: 1994
Title: Residues in Chaperonin Groel Required for Polypeptide Binding and Release
Authors: Fenton, W.A. / Kashi, Y. / Furtak, K. / Horwich, A.L.
History
DepositionMar 7, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROEL (HSP60 CLASS)
B: GROEL (HSP60 CLASS)
C: GROEL (HSP60 CLASS)
D: GROEL (HSP60 CLASS)
E: GROEL (HSP60 CLASS)
F: GROEL (HSP60 CLASS)
G: GROEL (HSP60 CLASS)


Theoretical massNumber of molelcules
Total (without water)400,9437
Polymers400,9437
Non-polymers00
Water0
1
A: GROEL (HSP60 CLASS)
B: GROEL (HSP60 CLASS)
C: GROEL (HSP60 CLASS)
D: GROEL (HSP60 CLASS)
E: GROEL (HSP60 CLASS)
F: GROEL (HSP60 CLASS)
G: GROEL (HSP60 CLASS)

A: GROEL (HSP60 CLASS)
B: GROEL (HSP60 CLASS)
C: GROEL (HSP60 CLASS)
D: GROEL (HSP60 CLASS)
E: GROEL (HSP60 CLASS)
F: GROEL (HSP60 CLASS)
G: GROEL (HSP60 CLASS)


Theoretical massNumber of molelcules
Total (without water)801,88514
Polymers801,88514
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-107 kcal/mol
Surface area150740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.000, 203.000, 278.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.626336, -0.779372, -0.017194), (0.779169, 0.626571, -0.017844), (0.024686, -0.002224, 0.999696)-16.2664, 34.1924, 1.30937
2given(-0.215469, -0.975993, -0.031778), (0.975851, -0.214014, -0.043724), (0.03587, -0.040431, 0.998538)-53.13586, 42.8365, 1.38949
3given(-0.90369, -0.427765, -0.019015), (0.428158, -0.902213, -0.051883), (0.005038, -0.055027, 0.998472)-83.2469, 18.588, 0.2694
4given(-0.900251, 0.435285, 0.008735), (-0.435197, -0.899135, -0.046462), (-0.012371, -0.045629, 0.998882)-83.09367, -18.94732, -0.42477
5given(-0.227259, 0.973422, 0.028333), (-0.973604, -0.226476, -0.028347), (-0.021177, -0.034028, 0.999196)-53.71845, -42.6244, -1.0386
6given(0.620408, 0.783927, 0.023486), (-0.7839, 0.620761, -0.012492), (-0.024372, -0.01066, 0.999646)-16.40549, -34.33678, -0.95095
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 6 .. 523 ? 6 .. ? 523 M2 6 .. 523 ? 6 .. ? 523 M3 6 .. 523 ? 6 .. ? 523 M4 6 .. 523 ? 6 .. ? 523 M5 6 .. 523 ? 6 .. ? 523 M6 6 .. 523 ? 6 .. ? 523 THESE TRANSFORMATIONS WILL YIELD APPROXIMATE COORDINATES FOR ONE GROEL 7MER WHEN APPLIED TO THE MONOMER COORDINATES IN THIS ENTRY. THIS STRICT NON-CRYSTALLOGRAPHIC SYMMETRY WAS USED IN THE REFINEMENT.

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Components

#1: Protein
GROEL (HSP60 CLASS)


Mass: 57277.531 Da / Num. of mol.: 7 / Mutation: R13G, A126V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5 / Plasmid: IQ-TRC / Gene (production host): GROEL / Production host: Escherichia coli (E. coli) / References: UniProt: P06139, UniProt: P0A6F5*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal grow
*PLUS
Temperature: 28 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlGroEL1drop
20.2 %(w/v)PEG80001drop
30.86 Mammonium sulfate1drop
42 mM1dropCaCl2
550 mMTris-acetate1drop
60.4 %(w/v)PEG80001reservoir
71.72 Mammonium sulfate1reservoir
84 mM1reservoirCaCl2
9100 mMTris-acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 117943 / % possible obs: 88.2 % / Observed criterion σ(I): 2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.368 -
Rwork0.326 -
obs0.326 110449
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23996 0 0 0 23996
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_deg1.12
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_d
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

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