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Open data
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Basic information
Entry | Database: PDB / ID: 1bhn | ||||||
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Title | NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE TRANSFERASE | ||||||
![]() | PHOSPHOTRANSFERASE | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / endocytosis / nervous system development / cell differentiation / ATP binding / nucleus ...nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / endocytosis / nervous system development / cell differentiation / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ladner, J.E. / Abdulaev, N.G. / Kakuev, D.L. / Karaschuk, G.N. / Tordova, M. / Eisenstein, E. / Fujiwara, J.H. / Ridge, K.D. / Gilliland, G.L. | ||||||
![]() | ![]() Title: The three-dimensional structures of two isoforms of nucleoside diphosphate kinase from bovine retina. Authors: Ladner, J.E. / Abdulaev, N.G. / Kakuev, D.L. / Tordova, M. / Ridge, K.D. / Gilliland, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.3 KB | Display | ![]() |
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PDB format | ![]() | 166.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 83.9 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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Unit cell |
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Components
#1: Protein | Mass: 17284.955 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-35G / #3: Chemical | ChemComp-GDP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.16 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop contains equal volume of the reservoir solution | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 15, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 41872 / % possible obs: 79 % / Redundancy: 4 % / Rsym value: 0.122 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.4→2.51 Å / Mean I/σ(I) obs: 1.4 / % possible all: 60 |
Reflection | *PLUS Num. measured all: 165667 / Rmerge(I) obs: 0.122 |
Reflection shell | *PLUS Lowest resolution: 2.54 Å / % possible obs: 60 % / Rmerge(I) obs: 0.384 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PARTIALLY REFINED STRUCTURE OF THE B ISOFORM Resolution: 2.4→20 Å / Isotropic thermal model: TNT BCORREL
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Solvent computation | Bsol: 231.6 Å2 / ksol: 0.672 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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