+Open data
-Basic information
Entry | Database: PDB / ID: 1zs6 | ||||||
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Title | structure of human nucleoside-diphosphate kinase 3 | ||||||
Components | Nucleoside diphosphate kinase 3Nucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / nucleotide metabolism / apoptosis / kinase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / apoptotic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Choe, J. / Dimov, S. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Structure of human nucleoside-diphosphate kinase 3 Authors: Dimov, S. / Choe, J. / ARROWSMITH, C. / EDWARDS, A. / SUNDSTROM, M. / BOCHKAREV, A. / PARK, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zs6.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zs6.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/1zs6 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/1zs6 | HTTPS FTP |
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-Related structure data
Related structure data | 1be4S 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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Details | The molecule is a hexamer. The biological assembly is generated by the two fold axis: y,x,-z |
-Components
#1: Protein | Mass: 19041.047 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NME3 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13232, nucleoside-diphosphate kinase #2: Chemical | #3: 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: 2.2 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Sodium Citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2005 |
Radiation | Monochromator: CONFOCAL MAXFLUX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 21910 / Num. obs: 21910 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 29.67 Å2 / Rmerge(I) obs: 0.119 |
Reflection shell | Resolution: 2.3→2.38 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1BE4 Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.384 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.256 / 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: 22.305 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.361 Å / Total num. of bins used: 20
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