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Yorodumi- PDB-4bvp: Legionella pneumophila NTPDase1 crystal form II (closed) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bvp | ||||||
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Title | Legionella pneumophila NTPDase1 crystal form II (closed) in complex with heptamolybdate and octamolybdate | ||||||
Components | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I | ||||||
Keywords | HYDROLASE / APYRASE / PURINERGIC SIGNALLING / KEGGIN / TRANSITION STATE / ADPASE / CD39 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LEGIONELLA PNEUMOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 1.49 Å | ||||||
Authors | Zebisch, M. / Schaefer, P. / Straeter, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of Legionella Pneumophila Ntpdase1 in Complex with Polyoxometallates. Authors: Zebisch, M. / Krauss, M. / Schafer, P. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bvp.cif.gz | 341.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bvp.ent.gz | 292.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/4bvp ftp://data.pdbj.org/pub/pdb/validation_reports/bv/4bvp | 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41880.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5ZUA2 |
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-Non-polymers , 12 types, 484 molecules
#2: Chemical | ChemComp-NA / | ||||||||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-M27 / #8: Chemical | ChemComp-EDO / #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | #13: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | Details: 100MM NAMES PH 5.2, 11% PEG3350, 20MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→45.3 Å / Num. obs: 119751 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.4 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER / Resolution: 1.49→45.34 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.114 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.061 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.175 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→45.34 Å
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Refine LS restraints |
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