+Open data
-Basic information
Entry | Database: PDB / ID: 4r2n | ||||||
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Title | Crystal structure of Rv3772 in complex with its substrate | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 | 4r2n.cif.gz | 295.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r2n.ent.gz | 239.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r2n ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r2n | HTTPS FTP |
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-Related structure data
Related structure data | 4r5zSC 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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2 |
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Unit cell |
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-Components
#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 #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-PHE / #4: Chemical | ChemComp-EPE / #5: 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: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1M succinic acid, HEPES, 1% PEG2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 113605 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % |
Reflection shell | Resolution: 1.98→2.05 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R5Z Resolution: 1.98→48.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.455 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 78.08 Å2 / Biso mean: 26.68 Å2 / Biso min: 14.83 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→48.21 Å
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Refine LS restraints |
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