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Yorodumi- PDB-3vgs: Wild-type nucleoside diphosphate kinase derived from Halomonas sp. 593 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vgs | ||||||
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Title | Wild-type 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 / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / 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 | 3vgs.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vgs.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/3vgs ftp://data.pdbj.org/pub/pdb/validation_reports/vg/3vgs | HTTPS FTP |
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-Related structure data
Related structure data | 3vgtC 3vguC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15284.089 Da / Num. of mol.: 2 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: 5.02 Å3/Da / Density % sol: 75.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE TRIBASIC DEHYDRATE, 30% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→77.08 Å / Num. obs: 25691 / % possible obs: 97.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NHK Resolution: 2.3→35.35 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.235 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.204 / 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: 48.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→35.35 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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