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Yorodumi- PDB-5yih: Crystal structure of tetrameric Nucleoside diphosphate kinase at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yih | ||||||
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Title | Crystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from Acinetobacter baumannii | ||||||
Components | Nucleoside diphosphate kinase | ||||||
Keywords | TRANSFERASE / Kinase | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Bairagya, H.R. / Sikarwar, J. / Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of tetrameric Nucleoside diphosphate kinase at 1.98 A resolution from Acinetobacter baumannii Authors: Bairagya, H.R. / Sikarwar, J. / Iqbal, N. / Singh, P.K. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yih.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yih.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/5yih ftp://data.pdbj.org/pub/pdb/validation_reports/yi/5yih | HTTPS FTP |
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-Related structure data
Related structure data | 4s0mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15483.479 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: ndk, F911_03401, HMPREF0010_01731 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CAF1, nucleoside-diphosphate kinase #2: Chemical | ChemComp-MG / #3: 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: 2.69 Å3/Da / Density % sol: 54.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES: 7.5, PEG3350, 0.1MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 5, 2017 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→68.8 Å / Num. obs: 45707 / % possible obs: 98.7 % / Redundancy: 3 % / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.98→2.009 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2261 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S0M Resolution: 1.98→68.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.085 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.17 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.989 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→68.8 Å
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Refine LS restraints |
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