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- PDB-1aon: CRYSTAL STRUCTURE OF THE ASYMMETRIC CHAPERONIN COMPLEX GROEL/GROE... -

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Basic information

Entry
Database: PDB / ID: 1aon
TitleCRYSTAL STRUCTURE OF THE ASYMMETRIC CHAPERONIN COMPLEX GROEL/GROES/(ADP)7
Components
  • GROEL/GROES COMPLEX
  • GROEL
KeywordsCOMPLEX (GROEL/GROES) / COMPLEX (GROEL-GROES) / CHAPERONIN ASSISTED PROTEIN FOLDING / COMPLEX (GROEL-GROES) complex
Function / homologyTCP-1-like chaperonin intermediate domain superfamily / Chaperonin 10 Kd subunit / GroEL-like apical domain superfamily / GroES chaperonin family / Chaperonin Cpn60, conserved site / Chaperonin GroES, conserved site / GroES-like superfamily / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / GroES chaperonin superfamily ...TCP-1-like chaperonin intermediate domain superfamily / Chaperonin 10 Kd subunit / GroEL-like apical domain superfamily / GroES chaperonin family / Chaperonin Cpn60, conserved site / Chaperonin GroES, conserved site / GroES-like superfamily / Chaperonin Cpn60/TCP-1 family / Chaperonin Cpn60 / GroES chaperonin superfamily / GroEL-like equatorial domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonins cpn60 signature. / Chaperonins cpn10 signature. / GroEL-GroES complex / 'de novo' protein folding / chaperone cofactor-dependent protein refolding / virion assembly / protein folding / response to radiation / unfolded protein binding / chaperone binding / response to heat / protein refolding / ATPase activity / cell cycle / cell division / magnesium ion binding / membrane / ATP binding / identical protein binding / metal ion binding / cytosol / 60 kDa chaperonin / 10 kDa chaperonin
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3 Å resolution
AuthorsXu, Z. / Horwich, A.L. / Sigler, P.B.
Citation
Journal: Nature / Year: 1997
Title: The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex.
Authors: Z Xu / A L Horwich / P B Sigler
#1: Journal: Nature / Year: 1997
Title: Distinct Actions of Cis and Trans ATP within the Double Ring of the Chaperonin Groel
Authors: Rye, H.S. / Burston, S.G. / Fenton, W.A. / Beechem, J.M. / Xu, Z. / Sigler, P.B. / Horwich, A.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 8, 1997 / Release: Oct 15, 1997
RevisionDateData content typeGroupProviderType
1.0Oct 15, 1997Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROEL
B: GROEL
C: GROEL
D: GROEL
E: GROEL
F: GROEL
G: GROEL
H: GROEL
I: GROEL
J: GROEL
K: GROEL
L: GROEL
M: GROEL
N: GROEL
O: GROEL/GROES COMPLEX
P: GROEL/GROES COMPLEX
Q: GROEL/GROES COMPLEX
R: GROEL/GROES COMPLEX
S: GROEL/GROES COMPLEX
T: GROEL/GROES COMPLEX
U: GROEL/GROES COMPLEX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)877,61435
Polyers874,45421
Non-polymers3,16114
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)69480
ΔGint (kcal/M)-486
Surface area (Å2)314810
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)255.260, 265.250, 184.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide
GROEL / / 60 KD CHAPERONIN / PROTEIN CPN60


Mass: 57260.504 Da / Num. of mol.: 14 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Strain: DH5 / Cell line: BL21 / Gene: GROE / Plasmid name: IQ-TRC / Genus (production host): Escherichia / Gene (production host): GROEL / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P0A6F5
#2: Protein/peptide
GROEL/GROES COMPLEX / 10 KD CHAPERONIN / PROTEIN CPN10


Mass: 10400.938 Da / Num. of mol.: 7 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Strain: DH5 / Cell line: BL21 / Gene: GROE / Plasmid name: PET11A / Genus (production host): Escherichia / Species (production host): Escherichia coli / Gene (production host): GROES / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6F9
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Formula: Mg / Magnesium
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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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: 3.5 / Density percent sol: 65 %
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG3000, 0.25M SODIUM GLUTAMATE, 100MM CACODYLIC ACID, PH 5.5
Crystal grow
*PLUS
Temp: 18 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
112 %PEG30001reservoir
20.25 Msodium glutamate1reservoir
3100 mMcacodylate1reservoir
46 %PEG30001drop
50.125 Msodium glutamate1drop
650 mMcacodylate1drop
77.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: NSLS BEAMLINE X25 / Synchrotron site: NSLS / Beamline: X25 / Wavelength: 0.95
DetectorType: MARRESEARCH / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Sep 1, 1996
RadiationMonochromator: TWO CRYSTAL NON-DISPERSIVE / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionD resolution high: 3 Å / D resolution low: 99 Å / Number obs: 242684 / Rsym value: 0.121 / NetI over sigmaI: 9.1 / Redundancy: 3.3 % / Percent possible obs: 96.7
Reflection shellHighest resolution: 3 Å / Lowest resolution: 3.14 Å / MeanI over sigI obs: 1.8 / Rsym value: 0.53 / Redundancy: 2.4 % / Percent possible all: 91.2
Reflection
*PLUS
Rmerge I obs: 0.121
Reflection shell
*PLUS
Number unique obs: 28317 / Percent possible obs: 91.2 / Rmerge I obs: 0.53

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEL
Details: RESIDUE 526 - 547 IN EACH GROEL CHAIN ARE ABSENT FROM THE MODEL BECAUSE THE ELECTRON DENSITY FOR THESE RESIDUES COULD NOT BE INTERPRETED. ARG 197, PHE 204, LYS 225, LYS 226, SER 228 - GLU 232, GLU 238 IN CHAINS A - G ARE MODELLED AS ALANINE.
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 61.5 Å2 / Aniso B11: 14.83 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 12.27 Å2 / Aniso B23: 0 Å2 / Aniso B33: -27.1 Å2
Least-squares processR factor R free: 0.291 / R factor R work: 0.248 / R factor obs: 0.248 / Highest resolution: 3 Å / Lowest resolution: 4 Å / Number reflection R free: 9846 / Number reflection obs: 198459 / Percent reflection R free: 5 / Percent reflection obs: 79.7
Refine analyzeLuzzati coordinate error free: 0.51 Å / Luzzati coordinate error obs: 0.45 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.65 Å / Luzzati sigma a obs: 0.58 Å
Refine hist #LASTHighest resolution: 3 Å / Lowest resolution: 4 Å
Number of atoms included #LASTProtein: 58688 / Nucleic acid: 0 / Ligand: 196 / Solvent: 0 / Total: 58884
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.010
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_deg1.472
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.711.5
X-RAY DIFFRACTIONx_mcangle_it4.322.0
X-RAY DIFFRACTIONx_scbond_it4.042.0
X-RAY DIFFRACTIONx_scangle_it6.002.5
Refine LS restraints ncsNcs model details: RESTRAINTS
Refine LS shellHighest resolution: 3 Å / R factor R free: 0.389 / R factor R work: 0.356 / Lowest resolution: 3.14 Å / Number reflection R free: 827 / Number reflection R work: 16487 / Total number of bins used: 8 / Percent reflection R free: 5 / Percent reflection obs: 56
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPARHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMTOPH19.PEP
X-RAY DIFFRACTION3PARAM19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.861 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71

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