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- PDB-1wnr: Crystal structure of the Cpn10 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1wnr
TitleCrystal structure of the Cpn10 from Thermus thermophilus HB8
Components10 kDa chaperonin
KeywordsCHAPERONE / CO-Chaperonin / protein CPN10 / Groes / Thermus Thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


protein folding / ATP binding / cytoplasm
Similarity search - Function
10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / GroES-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNumoto, N. / Kita, A. / Miki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of the Co-chaperonin Cpn10 from Thermus thermophilus HB8
Authors: Numoto, N. / Kita, A. / Miki, K.
History
DepositionAug 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 10 kDa chaperonin
B: 10 kDa chaperonin
C: 10 kDa chaperonin
D: 10 kDa chaperonin
E: 10 kDa chaperonin
F: 10 kDa chaperonin
G: 10 kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)72,1847
Polymers72,1847
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-42 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.881, 192.881, 109.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
10 kDa chaperonin


Mass: 10311.965 Da / Num. of mol.: 7 / Fragment: residues 1-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61493

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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: 3.54 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 300, potassium chloride, MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 17, 2003 / Details: DOUBLE FOCUSING MIRRORS
RadiationMonochromator: ROTATED-INCLINED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 22813 / Num. obs: 22805 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Rsym value: 0.069 / Net I/σ(I): 39.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 12 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 1932 / Rsym value: 0.358 / % possible all: 84.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HX5

1hx5


Resolution: 2.9→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2609897.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1148 5 %RANDOM
Rwork0.253 ---
all-22813 --
obs-22805 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.6778 Å2 / ksol: 0.338752 e/Å3
Displacement parametersBiso mean: 65.9 Å2
Baniso -1Baniso -2Baniso -3
1--19.26 Å20 Å20 Å2
2---19.26 Å20 Å2
3---38.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4211 0 0 0 4211
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.49
X-RAY DIFFRACTIONc_mcangle_it2.7
X-RAY DIFFRACTIONc_scbond_it2.11
X-RAY DIFFRACTIONc_scangle_it3.48
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.437 93 4.8 %
Rwork0.418 1839 -
obs-1932 84.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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