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Yorodumi- PDB-1z0s: Crystal structure of an NAD kinase from Archaeoglobus fulgidus in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z0s | ||||||
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Title | Crystal structure of an NAD kinase from Archaeoglobus fulgidus in complex with ATP | ||||||
Components | Probable inorganic polyphosphate/ATP-NAD kinase | ||||||
Keywords | TRANSFERASE / NAD kinase / ATP-binding / structural genomics / NAD / NADP / ATP / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC | ||||||
Function / homology | Function and homology information NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Liu, J. / Lou, Y. / Yokota, H. / Adams, P.D. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structures of an NAD Kinase from Archaeoglobus fulgidus in Complex with ATP, NAD, or NADP Authors: Liu, J. / Lou, Y. / Yokota, H. / Adams, P.D. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z0s.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z0s.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 1z0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/1z0s ftp://data.pdbj.org/pub/pdb/validation_reports/z0/1z0s | HTTPS FTP |
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-Related structure data
Related structure data | 1suwC 1z0uC 1z0zC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31039.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: ppnK / Plasmid: pB3.1114B / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O30297, NAD+ kinase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ATP / #4: Chemical | ChemComp-POP / #5: 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 Å3/Da / Density % sol: 36.7 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 7.5 Details: di-sodium phosphate, PEG3350, pH 7.5, EVAPORATION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 24, 2004 |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 104098 / Num. obs: 100976 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.7→1.73 Å / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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