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- PDB-2vhx: Crystal structure of the ternary complex of L-alanine dehydrogena... -
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Open data
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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 | |||||||||
![]() | ALANINE DEHYDROGENASE![]() | |||||||||
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Function / homology | ![]() alanine catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Agren, D. / Schneider, G. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 430.5 KB | Display | ![]() |
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PDB format | ![]() | 353.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P30234, UniProt: P9WQB1*PLUS, ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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