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- PDB-1sjp: Mycobacterium tuberculosis Chaperonin60.2 -

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Basic information

Entry
Database: PDB / ID: 1sjp
TitleMycobacterium tuberculosis Chaperonin60.2
Components60 kDa chaperonin 2
KeywordsCHAPERONE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


capsule / adhesion of symbiont to host / GroEL-GroES complex / positive regulation of transcription regulatory region DNA binding / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / host cell mitochondrion / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production ...capsule / adhesion of symbiont to host / GroEL-GroES complex / positive regulation of transcription regulatory region DNA binding / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / host cell mitochondrion / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / peptidoglycan-based cell wall / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / response to hypoxia / cell surface / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytoplasm / 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
Chaperonin GroEL 2 / Chaperonin GroEL 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsQamra, R. / Mande, S.C. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: J.Bacteriol. / Year: 2004
Title: Crystal Structure of the 65-Kilodalton Heat Shock Protein, Chaperonin 60.2, of Mycobacterium tuberculosis
Authors: Qamra, R. / Mande, S.C.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Mycobacterium tuberculosis GroEL homologues unusually exist as lower oligomers and retain the ability to suppress aggregation of substrate proteins
Authors: Qamra, R. / Srinivas, V. / Mande, S.C.
History
DepositionMar 4, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: 60 kDa chaperonin 2
B: 60 kDa chaperonin 2


Theoretical massNumber of molelcules
Total (without water)106,0982
Polymers106,0982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.674, 113.825, 79.535
Angle α, β, γ (deg.)90.00, 94.585, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 60 kDa chaperonin 2 / Chaperonin60


Mass: 53048.992 Da / Num. of mol.: 2 / Fragment: residues 42-539
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0440 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A520, UniProt: P9WPE7*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 56.77 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 17915 / Num. obs: 17489 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.99 % / Biso Wilson estimate: 88.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1705 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KP8.pdb

1kp8


Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.83 / SU B: 20.611 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2849 870 5.1 %RANDOM
Rwork0.24142 ---
all0.2436 17205 --
obs0.24359 16335 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 82.007 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å2-1.73 Å2
2---0.98 Å20 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6595 0 0 0 6595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226645
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9938981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0175888
X-RAY DIFFRACTIONr_chiral_restr0.0570.21103
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024818
X-RAY DIFFRACTIONr_nbd_refined0.2610.23583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.24
X-RAY DIFFRACTIONr_mcbond_it5.93734392
X-RAY DIFFRACTIONr_mcangle_it9.47567016
X-RAY DIFFRACTIONr_scbond_it8.755102253
X-RAY DIFFRACTIONr_scangle_it12.4201965
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 70
Rwork0.273 1179

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