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Yorodumi- PDB-2vhx: Crystal structure of the ternary complex of L-alanine dehydrogena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vhx | |||||||||
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Title | Crystal structure of the ternary complex of L-alanine dehydrogenase from Mycobacterium tuberculosis with NAD+ and pyruvate | |||||||||
Components | ALANINE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / NAD / SECRETED | |||||||||
Function / homology | Function and homology information alanine catabolic process / alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / cell wall / peptidoglycan-based cell wall / response to hypoxia / nucleotide binding / extracellular region / metal ion binding ...alanine catabolic process / alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / cell wall / peptidoglycan-based cell wall / response to hypoxia / nucleotide binding / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Agren, D. / Schneider, G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Three-Dimensional Structures of Apo- and Holo-L-Alanine Dehydrogenase from Mycobacterium Tuberculosis Reveal Conformational Changes Upon Coenzyme Binding. Authors: Agren, D. / Stehr, M. / Berthold, C.L. / Kapoor, S. / Oehlmann, W. / Singh, M. / Schneider, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vhx.cif.gz | 430.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vhx.ent.gz | 353.8 KB | Display | PDB format |
PDBx/mmJSON format | 2vhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/2vhx ftp://data.pdbj.org/pub/pdb/validation_reports/vh/2vhx | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39581.961 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P30234, UniProt: P9WQB1*PLUS, alanine dehydrogenase #2: Chemical | #3: Chemical | ChemComp-PYR / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | EXPRESSED WITH A C-TERMINAL 6XHIS TAG. | |
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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: 3 Å3/Da / Density % sol: 58.63 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 9, 2007 |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.2 Å / Num. obs: 182162 / % possible obs: 91 % / Observed criterion σ(I): 1.8 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.8 / % possible all: 67.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.073 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A RESIDUES 241-245 ARE MISSING. CHAIN B RESIDUES 240-244 ARE MISSING. CHAIN C RESIDUES 241-246 ARE MISSING. CHAIN D RESIDUES 240-244 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A RESIDUES 241-245 ARE MISSING. CHAIN B RESIDUES 240-244 ARE MISSING. CHAIN C RESIDUES 241-246 ARE MISSING. CHAIN D RESIDUES 240-244 ARE MISSING. THE PYRUVATE BOUND IN CHAIN E AND F ARE NOT BOUND AT FULL OCCUPANCY, SEE THE PAPER IN REFERENCES FOR FURTHER EXPLANATIONS.
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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: 17.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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