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- PDB-3m6c: Crystal structure of Mycobacterium tuberculosis GroEL1 apical domain -

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Basic information

Entry
Database: PDB / ID: 3m6c
TitleCrystal structure of Mycobacterium tuberculosis GroEL1 apical domain
Components60 kDa chaperonin 1
KeywordsCHAPERONE / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


nucleoid organization / bacterial nucleoid / GroEL-GroES complex / DNA protection / positive regulation of transcription regulatory region DNA binding / cell wall / chaperone cofactor-dependent protein refolding / unfolded protein binding / protein folding / single-stranded DNA binding ...nucleoid organization / bacterial nucleoid / GroEL-GroES complex / DNA protection / positive regulation of transcription regulatory region DNA binding / cell wall / chaperone cofactor-dependent protein refolding / unfolded protein binding / protein folding / single-stranded DNA binding / response to heat / protein refolding / cell surface / ATP binding / plasma membrane
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
60 kDa chaperonin 1 / 60 kDa chaperonin 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsTsai, F.T.F. / Sielaff, B. / Lee, K.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural and functional conservation of Mycobacterium tuberculosis GroEL paralogs suggests that GroEL1 Is a chaperonin.
Authors: Sielaff, B. / Lee, K.S. / Tsai, F.T.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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: 60 kDa chaperonin 1


Theoretical massNumber of molelcules
Total (without water)20,7471
Polymers20,7471
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.468, 78.647, 34.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 60 kDa chaperonin 1 / Protein Cpn60-1 / groEL protein 1


Mass: 20746.693 Da / Num. of mol.: 1 / Fragment: unp residues 184-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: groEL-1, groEL1, groL1, MT3526, MTCY78.12, Rv3417c / Plasmid: pProEX Htb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P0A518, UniProt: P9WPE9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% PEG 6000, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 12, 2008 / Details: Mirrors Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 10994 / % possible obs: 98.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.101 / Χ2: 1.087 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.367 / Num. unique all: 986 / Χ2: 0.924 / % possible all: 91.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SJP

1sjp


Resolution: 2.2→20.41 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 375010 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 544 5.2 %RANDOM
Rwork0.21 ---
obs-10517 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.122 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 65.66 Å2 / Biso mean: 30.293 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---3.87 Å20 Å2
3---4.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→20.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 0 65 1526
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it4.122.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 68 4.5 %
Rwork0.25 1458 -
all-1526 -
obs--84.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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