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- PDB-4uof: Crystallographic structure of nucleoside diphosphate kinase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4uof | ||||||
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Title | Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dADP | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | TRANSFERASE / BINARY / COMPLEX / DADP / PURINE / WHITE-SHRIMP / BINDING SITE / DESOXYNUCLEOTIDE | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lopez-Zavala, A.A. / Stojanoff, V. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. | ||||||
![]() | ![]() Title: Structure of Nucleoside Diphosphate Kinase from the Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates Authors: Lopez-Zavala, A.A. / Quintero-Reyez, I.E. / Carrasco-Miranda, J.S. / Stojanoff, V. / Weichsel, A. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.7 KB | Display | ![]() |
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PDB format | ![]() | 84.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uogC ![]() 4uohC ![]() 1be4S C: citing same article ( S: Starting model for refinement |
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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: 17015.627 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PJEXPRESS414 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.2 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% (W/V) PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 1, 2013 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.8 Å / Num. obs: 26320 / % possible obs: 91.2 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Biso Wilson estimate: 20.42 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.7 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BE4 Resolution: 2.102→19.854 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 24.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.102→19.854 Å
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Refine LS restraints |
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LS refinement shell |
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