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- PDB-1kp8: Structural Basis for GroEL-assisted Protein Folding from the Crys... -

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Basic information

Entry
Database: PDB / ID: 1kp8
TitleStructural Basis for GroEL-assisted Protein Folding from the Crystal Structure of (GroEL-KMgATP)14 at 2.0 A Resolution
ComponentsgroEL protein
KeywordsCHAPERONE / chaperonin / GroEL / assisted protein folding
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation ...GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / protein folding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / Chaperonin GroEL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWang, J.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structural Basis for GroEL-assisted Protein Folding from the Crystal Structure of (GroEL-KMgATP)14 at 2.0 A Resolution
Authors: Wang, J. / Boisvert, D.C.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: The 2.4 A Crystal Structure of the Bacterial Chaperonin GroEL Complexed with ATP Gamma S
Authors: Boisvert, D.C. / Wang, J. / Otwinowski, Z. / Horwich, A.L. / Sigler, P.B.
#2: Journal: Nature / Year: 1994
Title: The Crystal Structure of the Bacterial Chaperonin GroEL at 2.8 A
Authors: Braig, K. / Otwinowski, Z. / Hegde, R. / Boisvert, D.C. / Joachimiak, A. / Horwich, A.L. / Sigler, P.B.
#3: Journal: Nat.Struct.Biol. / Year: 1995
Title: Conformational Variability in the Refined Structure of the Chaperonin GroEL at 2.8 A Resolution
Authors: Braig, K. / Adams, P.D. / Brunger, A.T.
#4: Journal: Nature / Year: 1997
Title: The Crystal Structure of the Asymmetric GroEL-GroES-(ADP)7 Chaperonin Complex
Authors: Xu, Z. / Horwich, A.L. / Sigler, P.B.
History
DepositionDec 30, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionMar 25, 2003ID: 1DER
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2014Group: Non-polymer description / Version format compliance
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: groEL protein
B: groEL protein
C: groEL protein
D: groEL protein
E: groEL protein
F: groEL protein
G: groEL protein
H: groEL protein
I: groEL protein
J: groEL protein
K: groEL protein
L: groEL protein
M: groEL protein
N: groEL protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)810,23080
Polymers799,82514
Non-polymers10,40566
Water45,7762541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area68470 Å2
ΔGint-768 kcal/mol
Surface area292780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.571, 260.112, 150.200
Angle α, β, γ (deg.)90.00, 101.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 14 molecules ABCDEFGHIJKLMN

#1: Protein
groEL protein / 60 kDa chaperonin / Protein Cpn60 / groEL protein / AMS


Mass: 57130.379 Da / Num. of mol.: 14 / Mutation: R13G, A126V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5

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Non-polymers , 5 types, 2607 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2541 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.13 %
Description: The diffraction data used in remark 200 was extracted from PDB entry 1der.
Crystal grow
*PLUS
Method: other / Details: Ranson, N.A., (1998) Biochem. J., 333, 233.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 646053 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.096
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 540791 / % possible obs: 99.1 % / Num. measured all: 645898 / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→39.89 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 249116.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: This entry extends resolution from the previous 2.4A of PDB entry 1der to current 2.0A using the previous experimental data of 1der.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 10647 2 %RANDOM
Rwork0.243 ---
obs-540791 78.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.3657 Å2 / ksol: 0.352588 e/Å3
Displacement parametersBiso mean: 73.4 Å2
Baniso -1Baniso -2Baniso -3
1--11.7 Å20 Å21.84 Å2
2---1.09 Å20 Å2
3---12.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53970 0 574 2541 57085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.495 1190 1.9 %
Rwork0.519 60087 -
obs--53.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3ATP.PARATP.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
X-RAY DIFFRACTION5SO4.PARSO4.TOP
Refinement
*PLUS
Rfactor Rfree: 0.2579 / Rfactor Rwork: 0.2428
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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