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Yorodumi- PDB-2f6l: X-ray structure of Chorismate Mutase from Mycobacterium Tuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f6l | ||||||
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Title | X-ray structure of Chorismate Mutase from Mycobacterium Tuberculosis | ||||||
Components | Chorismate mutase | ||||||
Keywords | ISOMERASE / helical / dimer | ||||||
Function / homology | Function and homology information salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / extracellular region Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kim, S.K. / Howard, A.J. / Gilliland, G.L. / Reddy, P.T. / Ladner, J.E. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2006 Title: Biochemical and structural characterization of the secreted chorismate mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ enzyme not regulated by the aromatic amino acids. Authors: Kim, S.K. / Reddy, S.K. / Nelson, B.C. / Vasquez, G.B. / Davis, A. / Howard, A.J. / Patterson, S. / Gilliland, G.L. / Ladner, J.E. / Reddy, P.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f6l.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f6l.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2f6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/2f6l ftp://data.pdbj.org/pub/pdb/validation_reports/f6/2f6l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18495.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1885c / Production host: Escherichia coli (E. coli) References: UniProt: O07746, UniProt: P9WIB9*PLUS, chorismate mutase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Reservoir solution: 0.10 M MES pH 6.5, 30% Polyethylene glycol 8K. Protein solution: 50mM Tris pH 7.5, 1mM EDTA, 1mM DTT, 200mM sodium chloride. Protein concentration was 8.3 mg/ml., VAPOR ...Details: Reservoir solution: 0.10 M MES pH 6.5, 30% Polyethylene glycol 8K. Protein solution: 50mM Tris pH 7.5, 1mM EDTA, 1mM DTT, 200mM sodium chloride. Protein concentration was 8.3 mg/ml., VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 16, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→23 Å / Num. obs: 40279 / % possible obs: 98.6 % / Redundancy: 7.35 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / % possible all: 97.7 |
-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Partially refined structure of chorismate mutase from Yersinia pestis Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.142 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.112 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.181 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.791 Å / Total num. of bins used: 10
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