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- PDB-4r8d: Crystal structure of Rv1600 encoded aminotransferase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4r8d | ||||||
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Title | Crystal structure of Rv1600 encoded aminotransferase in complex with PLP-MES from Mycobacterium tuberculosis | ||||||
![]() | Histidinol-phosphate aminotransferase | ||||||
![]() | TRANSFERASE / Histidinol phosphate Aminotransferase | ||||||
Function / homology | ![]() histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / peptidoglycan-based cell wall / pyridoxal phosphate binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nasir, N. / Anant, A. / Vyas, R. / Biswal, B.K. | ||||||
![]() | ![]() Title: Crystal structure of Rv1600 encoded aminotransferase in complex with PLP-MES from Mycobacterium tuberculosis Authors: Nasir, N. / Anant, A. / Vyas, R. / Biswal, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.3 KB | Display | ![]() |
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PDB format | ![]() | 121.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.5 KB | Display | ![]() |
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Full document | ![]() | 488.3 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 42 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cq5S 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
#1: Protein | Mass: 42278.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H37Rv / Gene: hisC, P425_01659, RVBD_1600 / Plasmid: pYUB1062 / Production host: ![]() References: UniProt: I6XYD8, UniProt: P9WML7*PLUS, histidinol-phosphate transaminase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Ammonium sulfate, 0.1M MES monohydrate, 30% PEG MME 5000, 50 micro-molar PLP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40.19 Å / Num. all: 50285 / Num. obs: 47586 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.102 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 2.2 % / Num. unique all: 3385 / Rsym value: 0.351 / % possible all: 68.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CQ5 Resolution: 2.05→40.19 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.961 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 38.817 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→40.19 Å
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Refine LS restraints |
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