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Yorodumi- PDB-2x9q: Structure of the Mycobacterium tuberculosis protein, Rv2275, demo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x9q | ||||||
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Title | Structure of the Mycobacterium tuberculosis protein, Rv2275, demonstrates that cyclodipeptide synthetases are related to type I tRNA-Synthetases. | ||||||
Components | CYCLODIPEPTIDE SYNTHETASE | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information cyclo(L-tyrosyl-L-tyrosyl) synthase / ligase activity, forming carbon-oxygen bonds / aminoacyltransferase activity Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å | ||||||
Authors | Vetting, M.W. / Hegde, S.S. / Blanchard, J.S. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2010 Title: The Structure and Mechanism of the Mycobacterium Tuberculosis Cyclodityrosine Synthetase. Authors: Vetting, M.W. / Hegde, S.S. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x9q.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x9q.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/2x9q ftp://data.pdbj.org/pub/pdb/validation_reports/x9/2x9q | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9028, -0.1225, -0.4122), Vector: |
-Components
#1: Protein | Mass: 31901.900 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q50688, UniProt: P9WPF9*PLUS #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: 2.99 Å3/Da / Density % sol: 58.8 % / Description: NONE |
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Crystal grow | pH: 8.75 Details: 12-15% (W/V) PEG 8000, 1M LICL, 100 MM TRIS/BICINE, PH 8.75 |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→39 Å / Num. obs: 49827 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.6 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.02→70.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.903 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-48, A212-A216, A285-289, B1-B48, B209- B222, B285-B289 ARE DISORDERED RESIDUE WITH MINIMAL SIDE CHAIN DENSITY AT TERMINI MAY BE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A1-48, A212-A216, A285-289, B1-B48, B209- B222, B285-B289 ARE DISORDERED RESIDUE WITH MINIMAL SIDE CHAIN DENSITY AT TERMINI MAY BE MODELED AS ALANINES OR GLYCINES.
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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: 32.091 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→70.18 Å
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Refine LS restraints |
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