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Yorodumi- PDB-3vgu: E134A mutant nucleoside diphosphate kinase derived from Halomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vgu | ||||||
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Title | E134A mutant nucleoside diphosphate kinase derived from Halomonas sp. 593 | ||||||
Components | Nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / HALOPHILIC / KINASE / FERREDOXIN FOLD / ATP-BINDING / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Halomonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Okazaki, N. / Yonezawa, Y. / Arai, S. / Matsumoto, F. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Tokunaga, M. / Kuroki, R. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase Authors: Arai, S. / Yonezawa, Y. / Okazaki, N. / Matsumoto, F. / Tamada, T. / Tokunaga, H. / Ishibashi, M. / Blaber, M. / Tokunaga, M. / Kuroki, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vgu.cif.gz | 221.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vgu.ent.gz | 180.6 KB | Display | PDB format |
PDBx/mmJSON format | 3vgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vgu_validation.pdf.gz | 480.9 KB | Display | wwPDB validaton report |
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Full document | 3vgu_full_validation.pdf.gz | 500.4 KB | Display | |
Data in XML | 3vgu_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 3vgu_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/3vgu ftp://data.pdbj.org/pub/pdb/validation_reports/vg/3vgu | HTTPS FTP |
-Related structure data
Related structure data | 3vgsC 3vgtC 3vgvC 1nhkS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15226.054 Da / Num. of mol.: 8 / Mutation: E134A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halomonas (bacteria) / Strain: 593 / Gene: NDK / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83WH5, nucleoside-diphosphate kinase #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: 2.37 Å3/Da / Density % sol: 48.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.18M CALCIUM ACETATE HYDRATE, 0.09M SODIUM CACODYLATE TRIHYDRATE, 16% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→90.54 Å / Num. obs: 47185 / % possible obs: 93.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.9 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NHK Resolution: 2.3→22.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.267 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 28.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→22.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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