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Yorodumi- PDB-2r9q: Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r9q | ||||||
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Title | Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens | ||||||
Components |
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Keywords | HYDROLASE / 2'-deoxycytidine 5'-triphosphate deaminase / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Zhang, R. / Dong, A. / Xu, X. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens. Authors: Zhang, R. / Dong, A. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. | ||||||
History |
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Remark 999 | SEQUENCE THE AUTHORS FOUND TWO PEPTIDE CHAINS X AND Y BOUND TO MOLECULES B AND C, RESPECTIVELY. ... SEQUENCE THE AUTHORS FOUND TWO PEPTIDE CHAINS X AND Y BOUND TO MOLECULES B AND C, RESPECTIVELY. SINCE THE CHAINS X AND Y ARE UNEXPECTED RESULTS FROM THE CRYSTAL STRUCTURE ANALYSIS, AUTHORS DO NOT KNOW THE EXACT SEQUENCE OF THESE PEPTIDES. THE SEQUENCE OF THE RESIDUES IN THESE TWO CHAINS HAS BEEN ASSIGNED BY THE AUTHORS ACCORDING TO THE ELECTRON DENSITY MAP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r9q.cif.gz | 519.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r9q.ent.gz | 428 KB | Display | PDB format |
PDBx/mmJSON format | 2r9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r9q_validation.pdf.gz | 474.7 KB | Display | wwPDB validaton report |
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Full document | 2r9q_full_validation.pdf.gz | 500.9 KB | Display | |
Data in XML | 2r9q_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 2r9q_validation.cif.gz | 78.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/2r9q ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r9q | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | Authors state that the biological unit of this protein is unknown |
-Components
#1: Protein | Mass: 40576.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Gene: dcd, AGR_C_764, Atu0434 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8UI65, UniProt: A9CKA1*PLUS #2: Protein/peptide | | Mass: 660.740 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide #3: Protein/peptide | | Mass: 854.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide #4: 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: 2.29 Å3/Da / Density % sol: 46.23 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M CaCl2, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97940, 0.97960 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2007 / Details: mirrors | |||||||||
Radiation | Monochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→46.78 Å / Num. all: 73588 / Num. obs: 69099 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 17.1 | |||||||||
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 0.8 / Num. unique all: 5433 / % possible all: 53.36 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→46.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.991 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.24 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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 mean: 56.968 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→46.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 36.771 Å / Origin y: 52.115 Å / Origin z: 19.641 Å
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Refinement TLS group |
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