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Yorodumi- PDB-4uoh: Crystallographic structure of nucleoside diphosphate kinase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uoh | ||||||
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Title | Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with ADP | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
Keywords | TRANSFERASE / BINARY / COMPLEX / ADP / PURINE / WHITE-SHRIMP / BINDING SITE / NUCLEOTIDE | ||||||
Function / homology | Function and homology information nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | LITOPENAEUS VANNAMEI (Pacific white shrimp) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å | ||||||
Authors | Lopez-Zavala, A.A. / Guevara-Hernandez, E. / Stojanoff, V. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2014 Title: Structure of Nucleoside Diphosphate Kinase from Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates Authors: Lopez-Zavala, A.A. / Quintero-Reyes, 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uoh.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uoh.ent.gz | 83.2 KB | Display | PDB format |
PDBx/mmJSON format | 4uoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/4uoh ftp://data.pdbj.org/pub/pdb/validation_reports/uo/4uoh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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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.) LITOPENAEUS VANNAMEI (Pacific white shrimp) Plasmid: PJEXPRESS414 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): SALT INDUCIBLE / References: UniProt: A5J299, 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: 2.1 Å3/Da / Density % sol: 42.5 % Description: THE STARTING MODEL WAS PREVIOUS LITOPENAEUS VANNAMEI NDK STRUCTURE COMPLEXED WITH DADP WHICH WILL BE DEPOSITED IN PDB |
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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: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 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→34.8 Å / Num. obs: 29462 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.4 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SHRIMP NDK STRUCTURE TO BE DEPOSITED Resolution: 2.007→34.887 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 24.19 / Stereochemistry target values: ML Details: NO ELECTRON DENSITY WAS FOUND FOR ADP IN THE CHAIN A ACTIVE SITE. ALSO NUCLEOTIDE BINDING LOOP IN CHAIN A THAT COMPRISE RESIDUES 44-66 WERE DISORDERED. THEREFORE, BOTH LIGAND AND DISORDERED ...Details: NO ELECTRON DENSITY WAS FOUND FOR ADP IN THE CHAIN A ACTIVE SITE. ALSO NUCLEOTIDE BINDING LOOP IN CHAIN A THAT COMPRISE RESIDUES 44-66 WERE DISORDERED. THEREFORE, BOTH LIGAND AND DISORDERED LOOP WERE NOT INCLUDED IN IN FINAL THE MODEL.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.007→34.887 Å
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Refine LS restraints |
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LS refinement shell |
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