+Open data
-Basic information
Entry | Database: PDB / ID: 1sjp | ||||||
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Title | Mycobacterium tuberculosis Chaperonin60.2 | ||||||
Components | 60 kDa chaperonin 2 | ||||||
Keywords | CHAPERONE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information capsule / adhesion of symbiont to host / positive regulation of transcription regulatory region DNA binding / GroEL-GroES complex / chaperonin ATPase / host cell mitochondrion / chaperone cofactor-dependent protein refolding / peptidoglycan-based cell wall / isomerase activity / ATP-dependent protein folding chaperone ...capsule / adhesion of symbiont to host / positive regulation of transcription regulatory region DNA binding / GroEL-GroES complex / chaperonin ATPase / host cell mitochondrion / chaperone cofactor-dependent protein refolding / peptidoglycan-based cell wall / isomerase activity / ATP-dependent protein folding chaperone / unfolded protein binding / protein refolding / response to heat / response to hypoxia / cell surface / ATP hydrolysis activity / extracellular region / ATP binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Qamra, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sjp.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sjp.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sjp_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 1sjp_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 1sjp_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 1sjp_validation.cif.gz | 45.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/1sjp ftp://data.pdbj.org/pub/pdb/validation_reports/sj/1sjp | HTTPS FTP |
-Related structure data
Related structure data | 1kp8S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 56.77 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KP8.pdb 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.007 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20 /
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