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Yorodumi- PDB-4bvo: Legionella pneumophila NTPDase1 crystal form VI (part-open) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bvo | ||||||
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Title | Legionella pneumophila NTPDase1 crystal form VI (part-open) in complex with polytungstate POM-1 | ||||||
Components | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I | ||||||
Keywords | HYDROLASE / APYRASE / ATPASE / PURINERGIC SIGNALLING / TWINNING / METAL CLUSTER / KEGGIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LEGIONELLA PNEUMOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 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 | 4bvo.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bvo.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bvo_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4bvo_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4bvo_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4bvo_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/4bvo ftp://data.pdbj.org/pub/pdb/validation_reports/bv/4bvo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41537.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5ZUA2, apyrase | ||
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#2: Chemical | ChemComp-TLA / | ||
#3: Chemical | ChemComp-E43 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 0.54 % / Description: NONE |
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Crystal grow | Details: 100MM TRIS PH 7.3, 200MM K NA TARTRATE, 18% PEG3350, 10MM POM1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9181 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9181 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.4 Å / Num. obs: 50327 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 14.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.1 |
-Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.7→124.44 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.195 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
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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: 24.184 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→124.44 Å
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Refine LS restraints |
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