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Yorodumi- PDB-3aaq: Crystal structure of Lp1NTPDase from Legionella pneumophila in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aaq | ||||||
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Title | Crystal structure of Lp1NTPDase from Legionella pneumophila in complex with the inhibitor ARL 67156 | ||||||
Components | Ectonucleoside triphosphate diphosphohydrolase I | ||||||
Keywords | HYDROLASE / Adenosine Triphosphatase / NTPDase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Vivian, J.P. / Beddoe, T. / Rossjohn, J. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Crystal Structure of a Legionella pneumophila Ecto -Triphosphate Diphosphohydrolase, A Structural and Functional Homolog of the Eukaryotic NTPDases Authors: Vivian, J.P. / Riedmaier, P. / Ge, H. / Le Nours, J. / Sansom, F.M. / Wilce, M.C.J. / Byres, E. / Dias, M. / Schmidberger, J.W. / Cowan, P.J. / d'Apice, A.J.F. / Hartland, E.L. / Rossjohn, J. / Beddoe, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aaq.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aaq.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 3aaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/3aaq ftp://data.pdbj.org/pub/pdb/validation_reports/aa/3aaq | HTTPS FTP |
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-Related structure data
Related structure data | 3aapSC 3aarC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40032.625 Da / Num. of mol.: 1 / Fragment: UNP residues 41-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / Gene: lpg1905 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q5ZUA2 |
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#2: Chemical | ChemComp-ARU / |
#3: Water | ChemComp-HOH / |
Sequence details | ACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE ...ACCORDING TO AUTHOR, RESIDUE 149VAL IS A NATURAL VARIANT OF UNIPROT/TREMBL Q5ZUA2, AND WILL BE REPORTED TO UNIPROT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.75 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20-24%(w/v) PEG 3350, 0.2M Na Formate, 0.1M Bis-Tris propane pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 30076 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AAP Resolution: 2→34.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.671 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 32.421 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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