+Open data
-Basic information
Entry | Database: PDB / ID: 3cai | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis Rv3778c protein | ||||||
Components | POSSIBLE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / Rv3778c / Aminotransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Covarrubias, A.S. / Larsson, A.M. / Jones, T.A. / Bergfors, T. / Mowbray, S.L. / Unge, T. | ||||||
Citation | Journal: To be published Title: Structure and biochemical function studies of Mycobacterium tuberculosis essential protein Rv3778c Authors: Covarrubias, A.S. / Larsson, A.M. / Jones, T.A. / Bergfors, T. / Mowbray, S.L. / Unge, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cai.cif.gz | 170.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cai.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3cai ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3cai | HTTPS FTP |
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-Related structure data
Related structure data | 1c0nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42852.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: rv3778c / Plasmid: pPCRT7/CT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) AI References: UniProt: P72044, UniProt: P9WQ67*PLUS, Transferases; Transferring nitrogenous groups; Transaminases #2: 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: 2.27 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: 14.4% PEG 5000, 100mM sodium acetate, 10mM NaCl, 100mM Tris-HCl pH 8.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30.95 Å / Num. obs: 70551 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.138 / Rsym value: 0.138 / Net I/σ(I): 3.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.397 / Cor.coef. Fo:Fc: 0.589
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C0N Resolution: 1.8→30.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.954 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.258 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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