+Open data
-Basic information
Entry | Database: PDB / ID: 4wbf | ||||||
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Title | Acinetobacter baumannii SDF NDK | ||||||
Components | Nucleoside diphosphate kinaseNucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / kinase | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Hu, Y. / Liu, Y. | ||||||
Citation | Journal: Prog.Biochem.Biophys. / Year: 2015 Title: Structural and Functional Characterization of Acinetobacter baumannii Nucleoside Diphosphate Kinase Authors: Hu, Y. / Feng, F. / Liu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wbf.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wbf.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 4wbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/4wbf ftp://data.pdbj.org/pub/pdb/validation_reports/wb/4wbf | HTTPS FTP |
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-Related structure data
Related structure data | 4w98SC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 15344.276 Da / Num. of mol.: 1 / Fragment: UNP residues 1-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: SDF / Gene: ndk, ABSDF3006 / Production host: Escherichia coli (E. coli) / References: UniProt: B0VKS3, nucleoside-diphosphate kinase |
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#2: 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: 3.08 Å3/Da / Density % sol: 60.11 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium malonate, HEPES, Jeffamine ED-2001 |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→47.11 Å / Num. obs: 6880 / % possible obs: 100 % / Redundancy: 6.2 % / Net I/σ(I): 7.3 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4W98 Resolution: 2.64→47.107 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→47.107 Å
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Refine LS restraints |
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LS refinement shell |
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