+Open data
-Basic information
Entry | Database: PDB / ID: 4r5z | ||||||
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Title | Crystal structure of Rv3772 encoded aminotransferase | ||||||
Components | Putative phenylalanine aminotransferase | ||||||
Keywords | TRANSFERASE / Aminotransferase | ||||||
Function / homology | Function and homology information histidinol-phosphate transaminase activity / Transferases; Transferring nitrogenous groups; Transaminases / L-histidine biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Nasir, N. / Anant, A. / Vyas, R. / Biswal, B.K. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Crystal structures of Mycobacterium tuberculosis HspAT and ArAT reveal structural basis of their distinct substrate specificities Authors: Nasir, N. / Anant, A. / Vyas, R. / Biswal, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r5z.cif.gz | 307.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r5z.ent.gz | 247.9 KB | Display | PDB format |
PDBx/mmJSON format | 4r5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/4r5z ftp://data.pdbj.org/pub/pdb/validation_reports/r5/4r5z | HTTPS FTP |
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-Related structure data
Related structure data | 4r2nC 3ffhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39704.230 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: pat, P425_03929, RVBD_3772 / Production host: Mycobacterium smegmatis (bacteria) References: UniProt: I6Y4H4, UniProt: P9WML5*PLUS, Transferases; Transferring nitrogenous groups; Transaminases |
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-Non-polymers , 5 types, 1275 molecules
#2: Chemical | ChemComp-SIN / #3: Chemical | ChemComp-PMP / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EPE / #6: Water | ChemComp-HOH / | |
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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: 3.7 Å3/Da / Density % sol: 66.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1M succinic acid, 0.1M HEPES, 1% PEG 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 11, 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: 1.95→30 Å / Num. obs: 167040 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rsym value: 0.143 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.9 % / Num. unique all: 15927 / Rsym value: 0.571 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FFH Resolution: 1.95→27.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.909 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.113 / 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: 29.961 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→27.41 Å
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