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- PDB-4v43: Structural and mechanistic basis for allostery in the bacterial c... -

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Basic information

Entry
Database: PDB / ID: 4v43
TitleStructural and mechanistic basis for allostery in the bacterial chaperonin GroEL
ComponentsGROEL PROTEIN
KeywordsCHAPERONE / Wild Type GroEL / ALLOSTERY
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
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
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsWang, J.
Citation
Journal: To be Published
Title: A GroEL/GroES complex structure revisited: the structure-based mechanism of ATP hydrolysis
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
DepositionJan 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1J4Z, 1KPO
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 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
O: GROEL PROTEIN
P: GROEL PROTEIN
Q: GROEL PROTEIN
R: GROEL PROTEIN
S: GROEL PROTEIN
T: GROEL PROTEIN
U: GROEL PROTEIN
V: GROEL PROTEIN
W: GROEL PROTEIN
X: GROEL PROTEIN
Y: GROEL PROTEIN
Z: GROEL PROTEIN
1: GROEL PROTEIN
2: GROEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)1,600,43728
Polymers1,600,43728
Non-polymers00
Water00
1
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


Theoretical massNumber of molelcules
Total (without water)800,21814
Polymers800,21814
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: GROEL PROTEIN
P: GROEL PROTEIN
Q: GROEL PROTEIN
R: GROEL PROTEIN
S: GROEL PROTEIN
T: GROEL PROTEIN
U: GROEL PROTEIN
V: GROEL PROTEIN
W: GROEL PROTEIN
X: GROEL PROTEIN
Y: GROEL PROTEIN
Z: GROEL PROTEIN
1: GROEL PROTEIN
2: GROEL PROTEIN


Theoretical massNumber of molelcules
Total (without water)800,21814
Polymers800,21814
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.666, 264.235, 294.799
Angle α, β, γ (deg.)90.00, 92.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57158.457 Da / Num. of mol.: 28 / Mutation: D398A
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorDetector: CCD / Date: Nov 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 217987 / % possible obs: 85.1 % / Observed criterion σ(I): -3 / Redundancy: 11.02 % / Rmerge(I) obs: 0.114
Reflection shellResolution: 3.5→3.62 Å / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 1.396 / % possible all: 51.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kp8

1kp8


Resolution: 3.52→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 9860 5 %RANDOM
Rwork0.291 ---
obs-198130 76.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.4049 Å2 / ksol: 0.231794 e/Å3
Displacement parametersBiso mean: 80.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.64 Å0.63 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å1.14 Å
Refinement stepCycle: LAST / Resolution: 3.52→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53998 0 0 0 53998
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.52→3.72 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.418 789 4.9 %
Rwork0.417 15157 -
obs--36.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2

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