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Yorodumi- PDB-4dhk: Crystal structure of a deoxycytidine triphosphate deaminase (dCTP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dhk | ||||||
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Title | Crystal structure of a deoxycytidine triphosphate deaminase (dCTP deaminase) from Burkholderia thailandensis | ||||||
Components | Deoxycytidine triphosphate deaminase | ||||||
Keywords | HYDROLASE / Burkholderia thailandensis / deaminase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / nucleotide binding Similarity search - Function | ||||||
Biological species | Burkholderia thailandensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.05 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dhk.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dhk.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 4dhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dhk_validation.pdf.gz | 448.9 KB | Display | wwPDB validaton report |
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Full document | 4dhk_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 4dhk_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4dhk_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/4dhk ftp://data.pdbj.org/pub/pdb/validation_reports/dh/4dhk | HTTPS FTP |
-Related structure data
Related structure data | 3d63C 3dahC 3eizC 3ej2C 3ek2C 3ezoC 3f0fC 3ftpC 3gk0C 3gk3C 3gvfC 3gwaC 3gweC 3imlC 3sz8C 3t4cC 3tmlC 3tmqC 3txyC 3u7jC 3ue9C 3uk1C 3uk2C 3undC 3uptC 3urrC 3uw1C 3uw2C 3uw3C 3v2iC 3v7nC 3v8hC 3v9oC 3v9pC 3vavC 4ddoC 4dfeC 4dheC 4dutC 4dz4C 4e4tC 4efiC 4eg0C 4egjC 4ek2C 4eqyC 4ewgC 4exqC 4f2gC 4f32C 4f3nC 4f3yC 4f4hC 4f7dC 4fk8C 4fryC 4g1kC 4g67C 4ghkC 4h3yC 4h3zC 4h4gC 3km3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21507.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: dcd, BTH_I0860 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T083, dCTP deaminase #2: Chemical | ChemComp-EDO / #3: 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: 2.65 Å3/Da / Density % sol: 53.67 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Internal tracking number 225926. JCSG+ well A2. 20.0% w/v PEG3000, 0.1M Ammonium citrate/citric acid, 20% Ethylene glycol Cryo. ButhA.00973.a.A1 PS01180 46.83mg/ml, pH 5.5, VAPOR DIFFUSION, ...Details: Internal tracking number 225926. JCSG+ well A2. 20.0% w/v PEG3000, 0.1M Ammonium citrate/citric acid, 20% Ethylene glycol Cryo. ButhA.00973.a.A1 PS01180 46.83mg/ml, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2011 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→69.44 Å / Num. all: 27772 / Num. obs: 27763 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.52 % / Biso Wilson estimate: 39.228 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 22.71 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: PDB entry 3km3 Resolution: 2.05→69.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.905 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES WITH TLS ADDED. 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: 39.189 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→69.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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