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- PDB-4lmp: Mycobacterium tuberculosis L-alanine dehydrogenase x-ray structur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4lmp | ||||||
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Title | Mycobacterium tuberculosis L-alanine dehydrogenase x-ray structure in complex with N6-methyl adenosine | ||||||
![]() | Alanine dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Structural Genomics / PSI-Biology / Susceptibility to Known Mtb Inhibitors / MTBI / Rossmann Fold / N6-methyl adenosine binding / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / N-methyladenosine / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, H.-B. / Hung, L.-W. / Goulding, C.W. / Terwilliger, T.C. / Kim, C.-Y. / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) | ||||||
![]() | ![]() Title: Drug target analysis by dye-ligand affinity chromatography Authors: Kim, H.-B. / Hung, L.-W. / Goulding, C.W. / Terwilliger, T.C. / Kim, C.-Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89 KB | Display | ![]() |
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PDB format | ![]() | 66.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 743 KB | Display | ![]() |
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Full document | ![]() | 746.5 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vhyS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38753.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-6MD / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 2M ammonium sulfate, 5% 2-propanol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2010 / Details: Si111 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 33325 / Num. obs: 33325 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 23.97 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 22.84 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.234 / Num. unique all: 1602 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VHY Resolution: 1.95→48.4 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.4 Å
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Refine LS restraints |
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LS refinement shell |
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