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Yorodumi- PDB-2vkl: X-ray crystal structure of the intracellular Chorismate mutase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vkl | ||||||
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Title | X-ray crystal structure of the intracellular Chorismate mutase from Mycobactrerium Tuberculosis in complex with malate | ||||||
Components | RV0948C/MT0975 | ||||||
Keywords | ISOMERASE / HELICAL / TUBERCULOSIS / INTRACELLULAR / CHORISMATE MUTASE | ||||||
Function / homology | Function and homology information aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Okvist, M. / Roderer, K. / Sasso, S. / Kast, P. / Krengel, U. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Structure and Function of a Complex between Chorismate Mutase and Dahp Synthase: Efficiency Boost for the Junior Partner. Authors: Sasso, S. / Okvist, M. / Roderer, K. / Gamper, M. / Codoni, G. / Krengel, U. / Kast, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vkl.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vkl.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 2vkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/2vkl ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vkl | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10107.812 Da / Num. of mol.: 1 / Fragment: RESIDUES 16-105 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PKTCMM-H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KA13 References: UniProt: P64767, UniProt: P9WIC1*PLUS, chorismate mutase |
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#2: Chemical | ChemComp-MLT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 21.5 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 0.1M MMT BUFFER PH 9, 25% W/V PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Oct 4, 2007 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20.76 Å / Num. obs: 9314 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 6.62 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.81 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 6.47 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→18.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.057 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→18.98 Å
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Refine LS restraints |
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