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- PDB-3q83: Crystal structure of Staphylococcus aureus nucleoside diphosphate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q83 | ||||||
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Title | Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase | ||||||
![]() | 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 / Metal binding / Phosphorylation / Kinase / Nucleotide metabolism | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / 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 | ![]() | 186 KB | Display | ![]() |
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PDB format | ![]() | 150.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3q86C ![]() 3q89C ![]() 3q8uC ![]() 3q8vC ![]() 3q8yC ![]() 1jxvS 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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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: 2 / 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.16 % |
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Crystal grow | Temperature: 298 K / Method: micobatch crystallization / pH: 4.6 Details: 0.1M MgCl2, 0.1M Na-Acetate, pH 4.6, 20% PEG 2000, Micobatch Crystallization, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2009 / Details: Grazing angle 2.8 mrad |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→72.36 Å / Num. obs: 30434 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4378 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1JXV Resolution: 2.5→45.81 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.846 / SU B: 10.569 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / 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: 16.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.345 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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