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Open data
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Basic information
Entry | Database: PDB / ID: 1ndk | ||||||
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Title | X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE![]() | ||||||
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Function / homology | ![]() dGTP biosynthetic process from dGDP / dGDP phosphorylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Janin, J. / Dumas, C. / Morera, S. / Lascu, I. / Veron, M. | ||||||
![]() | ![]() Title: X-ray structure of nucleoside diphosphate kinase. Authors: Dumas, C. / Lascu, I. / Morera, S. / Glaser, P. / Fourme, R. / Wallet, V. / Lacombe, M.L. / Veron, M. / Janin, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.4 KB | Display | ![]() |
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PDB format | ![]() | 27.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 234.9 KB | Display | ![]() |
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Full document | ![]() | 237.9 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 16781.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. obs: 9012 / % possible obs: 99.3 % / Num. measured all: 82562 / Rmerge(I) obs: 0.046 |
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Processing
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Refinement | Rfactor Rwork![]() Details: NO DENSITY IS SEEN FOR RESIDUES 1 - 7. DENSITY FOR RESIDUE 8 IS POOR. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 7 Å / Num. reflection obs: 8697 / Rfactor obs: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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