+Open data
-Basic information
Entry | Database: PDB / ID: 4c6a | ||||||
---|---|---|---|---|---|---|---|
Title | High Resolution Structure of the Nucleoside diphosphate kinase | ||||||
Components | NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLICNucleoside-diphosphate kinase | ||||||
Keywords | TRANSFERASE / PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / CTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / nucleoside triphosphate biosynthetic process / negative regulation of pinocytosis / nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / negative regulation of exocytosis / negative regulation of phagocytosis / GTP biosynthetic process / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / phosphorylation / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Priet, S. / Ferron, F. / Alvarez, K. / Verron, M. / Canard, B. | ||||||
Citation | Journal: Antiviral Res. / Year: 2015 Title: Enzymatic Synthesis of Acyclic Nucleoside Thiophosphonate Diphosphates: Effect of the Alpha-Phosphorus Configuration on HIV-1 RT Activity. Authors: Priet, S. / Roux, L. / Saez-Ayala, M. / Ferron, F. / Canard, B. / Alvarez, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4c6a.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4c6a.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 4c6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/4c6a ftp://data.pdbj.org/pub/pdb/validation_reports/c6/4c6a | HTTPS FTP |
---|
-Related structure data
Related structure data | 4cp5C 3fkbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16604.043 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P22887, nucleoside-diphosphate kinase |
---|---|
#2: Chemical | ChemComp-PEG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1 Å3/Da / Density % sol: 49.9 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 / Details: 26% PEG 1000, 100MM TRIS PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.95373 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→26.84 Å / Num. obs: 45344 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 21 % / Biso Wilson estimate: 9.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 46.1 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 20 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 10.6 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FKB Resolution: 1.25→26.84 Å / Cor.coef. Fo:Fc: 0.9522 / Cor.coef. Fo:Fc free: 0.9555 / SU R Cruickshank DPI: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.045 / SU Rfree Blow DPI: 0.043 / SU Rfree Cruickshank DPI: 0.039
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.69 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.115 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→26.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.25→1.28 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -53.3199 Å / Origin y: 29.2379 Å / Origin z: 121.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: CHAIN A |