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- PDB-3q8u: Crystal structure of Staphylococcus aureus nucleoside diphosphate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q8u | ||||||
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Title | Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP | ||||||
![]() | Nucleoside diphosphate kinase | ||||||
![]() | TRANSFERASE / Ferridoxin fold / alpha-beta protein family / Nucleoside diphosphate kinases (NDKs) catalyze the transfer of a gamma phosphate from nucleoside triphosphates to nucleoside diphosphate / Nucleotide binding / Magnesium / Metal binding / Phosphorylation | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Srivastava, S.K. / Rajasree, K. / Gopal, B. | ||||||
![]() | ![]() Title: Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase. Authors: Srivastava, S.K. / Rajasree, K. / Gopal, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.6 KB | Display | ![]() |
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PDB format | ![]() | 158.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 41.8 KB | Display | |
Data in CIF | ![]() | 56.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3q83SC ![]() 3q86C ![]() 3q89C ![]() 3q8vC ![]() 3q8yC S: Starting model for refinement C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 1 - 149 / Label seq-ID: 1 - 149
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Components
#1: Protein | Mass: 17663.873 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: genomic DNA Source: (gene. exp.) ![]() ![]() Strain: COL / Gene: ndk, SACOL1509 / Plasmid: pET22b / Production host: ![]() ![]() #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 298 K / Method: microbatch crystallization / pH: 6.5 Details: 0.1M Bis-Tris, 6.5, 25% PEG 2000, Microbatch Crystallization, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 19, 2010 / Details: VariMax |
Radiation | Monochromator: CuK (Alpha) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→34.52 Å / Num. obs: 44437 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 5.6 / Num. unique all: 5870 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q83 Resolution: 2.22→34.52 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.254 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.436 Å2
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Refine analyze | Luzzati coordinate error obs: 0.249 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→34.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1150 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.215→2.272 Å / Total num. of bins used: 20
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