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- PDB-2vhy: Crystal structure of apo L-alanine dehydrogenase from Mycobacteri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vhy | ||||||
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Title | Crystal structure of apo L-alanine dehydrogenase from Mycobacterium tuberculosis | ||||||
![]() | ALANINE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / NAD / SECRETED | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
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 | ![]() | 131.1 KB | Display | ![]() |
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PDB format | ![]() | 102.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.8 KB | Display | ![]() |
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Full document | ![]() | 455.1 KB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vhvC ![]() 2vhwC ![]() 2vhxC ![]() 2vhzC ![]() 1pjcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.97754, 0.21005, 0.01697), Vector: |
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Components
#1: Protein | Mass: 39581.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P30234, UniProt: P9WQB1*PLUS, alanine dehydrogenase #2: 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: 4.31 Å3/Da / Density % sol: 71.24 % / Description: NONE |
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Crystal grow | Details: 0.4M AMMONIUM BICARBONATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 6, 2006 / Details: RH-COATED TOROIDAL SI MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45 Å / Num. obs: 47413 / % possible obs: 97 % / Observed criterion σ(I): 2.9 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.34→2.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / % possible all: 79 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PJC Resolution: 2.3→45 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: LEAST SQUARES RESIDUAL FOR HEMIHEDRAL TWINNING Details: THE PROTOCOLL FOR HEMIHEDRALLY TWINNED DATA WAS USED. THE R-VALUES ARE FOR TWINNED DATA. RESIDUES A239-A258, A269-A294, A297-A301, B242-B255, B268- B293 AND B298-B301 ARE REMOVED FROM THE ...Details: THE PROTOCOLL FOR HEMIHEDRALLY TWINNED DATA WAS USED. THE R-VALUES ARE FOR TWINNED DATA. RESIDUES A239-A258, A269-A294, A297-A301, B242-B255, B268- B293 AND B298-B301 ARE REMOVED FROM THE MODEL SINCE THERE IS NO DENSITY FOR THESE RESIDUES.
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Solvent computation | Bsol: 50.2348 Å2 / ksol: 0.372117 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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