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Yorodumi- PDB-2vi7: Structure of a Putative Acetyltransferase (PA1377)from Pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vi7 | ||||||
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Title | Structure of a Putative Acetyltransferase (PA1377)from Pseudomonas aeruginosa | ||||||
Components | ACETYLTRANSFERASE PA1377 | ||||||
Keywords | TRANSFERASE / GNAT / GCN5 FAMILY / N-ACETYLTRANSFERASE / HYPOTHETICAL PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Davies, A.M. / Tata, R. / Chauviac, F.X. / Sutton, B.J. / Brown, P.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Structure of a Putative Acetyltransferase (Pa1377) from Pseudomonas Aeruginosa. Authors: Davies, A.M. / Tata, R. / Chauviac, F.X. / Sutton, B.J. / Brown, P.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vi7.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vi7.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vi7_validation.pdf.gz | 356.5 KB | Display | wwPDB validaton report |
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Full document | 2vi7_full_validation.pdf.gz | 360.1 KB | Display | |
Data in XML | 2vi7_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 2vi7_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/2vi7 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vi7 | HTTPS FTP |
-Related structure data
Related structure data | 2ge3S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 20097.773 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAC1 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I3W7 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-AZI / #5: 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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: HANGING DROP VAPOR DIFFUSION. RESERVOIR OF 500 MICROLITRES 0.1M TRIS-HCL AT PH6.5, 1.6M AMMONIUM SULFATE AND 0.1% SODIUM AZIDE. DROPS CONTAINED 1 MICROLITRE OF PROTEIN AT 13MG /ML AND AN ...Details: HANGING DROP VAPOR DIFFUSION. RESERVOIR OF 500 MICROLITRES 0.1M TRIS-HCL AT PH6.5, 1.6M AMMONIUM SULFATE AND 0.1% SODIUM AZIDE. DROPS CONTAINED 1 MICROLITRE OF PROTEIN AT 13MG /ML AND AN EQUAL VOLUME OF RESERVOIR. DROPS WERE KEPT AT 291K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→64.3 Å / Num. obs: 28683 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GE3 Resolution: 2.25→64.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: MOLECULES A AND B OF THE ASYMMETRIC UNIT FORM THE ASSUMED DIMERIC, BIOLOGICAL UNIT. MOLECULE C FORMS A DIMER WITH A MOLECULE RELATED BY CRYSTALLOGRAPHIC SYMMETRY.
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Solvent computation | Bsol: 42.52 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→64.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Num. reflection Rfree: 136 / Num. reflection Rwork: 2684 / Total num. of bins used: 10 |