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Yorodumi- PDB-2hrm: Crystal structure of dUTPase complexed with substrate analogue me... -
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-Basic information
Entry | Database: PDB / ID: 2hrm | ||||||
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Title | Crystal structure of dUTPase complexed with substrate analogue methylene-dUTP | ||||||
Components | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
Keywords | HYDROLASE / JELLY ROLL / ENZYME-SUBSTRATE ANALOGUE LIGAND COMPLEX | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / protein homotrimerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Barabas, O. / Kovari, J. / Tapai, R. / Vertessy, B.G. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site. Authors: Kovari, J. / Barabas, O. / Varga, B. / Bekesi, A. / Tolgyesi, F. / Fidy, J. / Nagy, J. / Vertessy, B.G. #1: Journal: J.Biol.Chem. / Year: 2004 Title: Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase. Authors: Barabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Atomic Resolution Structure of Escherichia Coli Dutpase Determined Ab Initio Authors: Gonzalez, A. / Larsson, G. / Persson, R. / Cedergren-Zeppezauer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hrm.cif.gz | 45.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hrm.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/2hrm ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hrm | HTTPS FTP |
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-Related structure data
Related structure data | 2hr6C 1euwS C: citing same article (ref.) 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 on special symmetry positions |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-y,1+x-y,z and -x+y,1-x,z |
-Components
#1: Protein | Mass: 16302.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dut / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06968, dUTP diphosphatase |
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#2: Chemical | ChemComp-UC5 / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 20% PEG 3350, 0.2M SODIUM ACETATE, 0.1M TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: mirror |
Radiation | Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.85 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 19276 / Num. obs: 19276 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.16 % / Biso Wilson estimate: 28.27 Å2 / Rsym value: 0.048 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.19 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3034 / Rsym value: 0.457 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EUW Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.355 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.045 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.703→1.747 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.5011 Å / Origin y: 15.8307 Å / Origin z: 4.9283 Å
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Refinement TLS group |
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