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Yorodumi- PDB-2j4h: Crystal structure of a H121A Escherichia coli dCTP deaminase muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j4h | ||||||
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Title | Crystal structure of a H121A Escherichia coli dCTP deaminase mutant enzyme | ||||||
Components | DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE | ||||||
Keywords | HYDROLASE / DCTP DEAMINASE / NUCLEOTIDE METABOLISM / TRIMER | ||||||
Function / homology | Function and homology information dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / protein homotrimerization / response to radiation / nucleotide binding / protein-containing complex ...dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / protein homotrimerization / response to radiation / nucleotide binding / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å | ||||||
Authors | Johansson, E. / Thymark, M. / Bynck, J.H. / Fanoe, M. / Larsen, S. / Willemoes, M. | ||||||
Citation | Journal: FEBS J. / Year: 2007 Title: Regulation of Dctp Deaminase from Escherichia Coli by Nonallosteric Dttp Binding to an Inactive Form of the Enzyme Authors: Johansson, E. / Thymark, M. / Bynck, J.H. / Fanoe, M. / Larsen, S. / Willemoes, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j4h.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j4h.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 2j4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j4h_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2j4h_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2j4h_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2j4h_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/2j4h ftp://data.pdbj.org/pub/pdb/validation_reports/j4/2j4h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.8738, 0.4863, 0.000542), Vector: |
-Components
#1: Protein | Mass: 21209.186 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P28248, dCTP deaminase #2: Chemical | #3: Chemical | ChemComp-MG / Compound details | ENGINEERED | |
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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: 2.55 Å3/Da / Density % sol: 51.39 % |
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Crystal grow | Method: vapor diffusion / pH: 6.8 Details: VAPOUR DIFFUSION, 34% PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH6.8, 5MM DCTP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.046 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 11, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.046 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 11131 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.3 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.605 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / 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 mean: 29.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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