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Yorodumi- PDB-2dxd: Crystal structure of nucleoside diphosphate kinase in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 2dxd | |||||||||
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Title | Crystal structure of nucleoside diphosphate kinase in complex with ATP analog | |||||||||
Components | Nucleoside diphosphate kinase | |||||||||
Keywords | TRANSFERASE / nucleoside binding / kinase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
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 | Pyrococcus horikoshii (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | |||||||||
Authors | Kato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of nucleoside diphosphate kinase in complex with ATP analog Authors: Kato-Murayama, M. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dxd.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dxd.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 2dxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dxd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2dxd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2dxd_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 2dxd_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/2dxd ftp://data.pdbj.org/pub/pdb/validation_reports/dx/2dxd | HTTPS FTP |
-Related structure data
Related structure data | 2cwkS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18342.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea) Species: Pyrococcus horikoshii Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: ndk, PH0698 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: O58429, nucleoside-diphosphate kinase #2: Chemical | #3: Chemical | #4: 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: 3.4 Å3/Da / Density % sol: 63.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na Citrate, Bicine, 10mM ANP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 27, 2005 |
Radiation | Monochromator: conforcal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→87.71 Å / Num. obs: 48556 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 1.77→1.83 Å / Rsym value: 0.317 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CWK Resolution: 1.77→37.15 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3225959.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8777 Å2 / ksol: 0.387272 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.77→37.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.85 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
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Xplor file |
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