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- PDB-1hx5: Crystal structure of M. tuberculosis chaperonin-10 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1hx5
TitleCrystal structure of M. tuberculosis chaperonin-10
Components10 KDA CHAPERONIN
KeywordsCHAPERONE / beta barrel / mobile loop / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


zymogen binding / cell wall / chaperone cofactor-dependent protein refolding / protein folding chaperone / peptidoglycan-based cell wall / unfolded protein binding / cellular response to heat / response to heat / protein-folding chaperone binding / response to antibiotic ...zymogen binding / cell wall / chaperone cofactor-dependent protein refolding / protein folding chaperone / peptidoglycan-based cell wall / unfolded protein binding / cellular response to heat / response to heat / protein-folding chaperone binding / response to antibiotic / regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular region / ATP binding / metal ion binding / plasma membrane / cytosol
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
Co-chaperonin GroES / Co-chaperonin GroES
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsTaneja, B. / Mande, S.C. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: CURR.SCI. / Year: 2001
Title: Three-dimensional Structure of Mycobacterium tuberculosis Chaperonin-10 Reveals a Partially Stable Conformation for its Mobile Loop
Authors: Taneja, B. / Mande, S.C.
#1: Journal: To be Published
Title: Crystal Structure of Mycobacterium tuberculosis Chaperonin-10 at 3.5 ang Resolution
Authors: Taneja, B. / Mande, S.C.
History
DepositionJan 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 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

Downloads & links

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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)74,7957
Polymers74,7957
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10930 Å2
ΔGint-86 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.5, 162.5, 125.6
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
10 KDA CHAPERONIN / PROTEIN CPN10


Mass: 10684.979 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: RV3418C / Plasmid: PMAL-C / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P09621, UniProt: P9WPE5*PLUS

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 400, lithium sulphate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
210 mM1dropCaCl2
326 %PEG4001reservoir
4210 mM1reservoirLi2SO4
5100 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 9954 / Num. obs: 9927 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 68.6 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.7
Reflection shellResolution: 3.5→3.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.28 / % possible all: 90.5
Reflection
*PLUS
Lowest resolution: 30 Å

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Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LEP

1lep


Resolution: 3.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 478 -Random
Rwork0.202 ---
all0.202 10332 --
obs0.202 9954 96.4 %-
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 0 0 4312
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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