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- PDB-3rtk: Crystal structure of Cpn60.2 from Mycobacterium tuberculosis at 2.8A -

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Basic information

Entry
Database: PDB / ID: 3rtk
TitleCrystal structure of Cpn60.2 from Mycobacterium tuberculosis at 2.8A
Components60 kDa chaperonin 2
KeywordsCHAPERONE / Heat shock protein / chaperonin
Function / homology
Function and homology information


capsule / adhesion of symbiont to host / GroEL-GroES complex / chaperonin ATPase / positive regulation of transcription regulatory region DNA binding / host cell mitochondrion / chaperone cofactor-dependent protein refolding / isomerase activity / peptidoglycan-based cell wall / ATP-dependent protein folding chaperone ...capsule / adhesion of symbiont to host / GroEL-GroES complex / chaperonin ATPase / positive regulation of transcription regulatory region DNA binding / host cell mitochondrion / chaperone cofactor-dependent protein refolding / isomerase activity / peptidoglycan-based cell wall / ATP-dependent protein folding chaperone / unfolded protein binding / response to heat / protein refolding / response to hypoxia / cell surface / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytosol / cytoplasm
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: 2.8 Å
AuthorsShahar, A. / Melamed-Frank, M. / Kashi, Y. / Adir, N.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The dimeric structure of the Cpn60.2 chaperonin of Mycobacterium tuberculosis at 2.8 A reveals possible modes of function.
Authors: Shahar, A. / Melamed-Frank, M. / Kashi, Y. / Shimon, L. / Adir, N.
History
DepositionMay 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,2693
Polymers115,2452
Non-polymers241
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 60 kDa chaperonin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6472
Polymers57,6221
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: 60 kDa chaperonin 2


Theoretical massNumber of molelcules
Total (without water)57,6221
Polymers57,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.190, 111.980, 77.280
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 60 kDa chaperonin 2 / Cpn60.2 / 65 kDa antigen / Antigen A / Cell wall protein A / GroEL protein 2 / Heat shock protein 65


Mass: 57622.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: groL2, groEL-2, groEL2, hsp65, Rv0440, MT0456, MTV037.04
Production host: Escherichia coli (E. coli) / References: UniProt: P0A520, UniProt: P9WPE7*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M HEPES, pH 7.5, 10% 2-propanol, 20% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 24284 / Num. obs: 23832 / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17.28
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.8-2.872.81.93166110.25
2.95-3.043.773.693319114.5
3.13-3.233.827.023169114
3.35-3.473.812.62927112.9
3.62-3.783.7818.362679112
3.96-4.183.7726.982449110
4.43-4.743.7432.03215419.3
5.11-5.63.732.57183317.87
6.26-7.233.6240.75141515.92
8.86-12.533.4245.1272112.84

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SJP

1sjp


Resolution: 2.8→20 Å / σ(F): 2.5
RfactorNum. reflectionSelection details
Rfree0.285 1105 RANDOM
Rwork0.217 --
all-24284 -
obs-23832 -
Displacement parametersBiso mean: 83.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6620 0 1 8 6629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.53
X-RAY DIFFRACTIONc_bond_d0.009

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