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Yorodumi- PDB-3h78: Crystal structure of Pseudomonas aeruginosa PqsD C112A mutant in ... -
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-Basic information
Entry | Database: PDB / ID: 3h78 | |||||||||
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Title | Crystal structure of Pseudomonas aeruginosa PqsD C112A mutant in complex with anthranilic acid | |||||||||
Components | PQS biosynthetic enzyme | |||||||||
Keywords | TRANSFERASE / PqsD / PQS / Anthranilic Acid / Anthraniloyl-CoA | |||||||||
Function / homology | Function and homology information anthraniloyl-CoA anthraniloyltransferase / secondary metabolite biosynthetic process / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Bera, A.K. / Atanasova, V. / Parsons, J.F. | |||||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structure of PqsD, a Pseudomonas quinolone signal biosynthetic enzyme, in complex with anthranilate. Authors: Bera, A.K. / Atanasova, V. / Robinson, H. / Eisenstein, E. / Coleman, J.P. / Pesci, E.C. / Parsons, J.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h78.cif.gz | 282 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h78.ent.gz | 228.8 KB | Display | PDB format |
PDBx/mmJSON format | 3h78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h78_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 3h78_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 3h78_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 3h78_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h78 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h78 | HTTPS FTP |
-Related structure data
Related structure data | 3h76C 3h77SC C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 38712.160 Da / Num. of mol.: 2 / Mutation: C112A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PA01 / 1C / PRS 101 / LMG 12228 / Gene: pqsD, PA0999 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P20582, beta-ketoacyl-[acyl-carrier-protein] synthase III #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | THE SYNONYM FOR 2-AMINOBENZO | |
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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: 1.96 Å3/Da / Density % sol: 37.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M MgCl2, 0.1M Tris-HCl pH 8.5, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 62039 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 7.1 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H77 Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.23 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.249 / ESU R Free: 0.108 / 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: 17.183 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.742 Å / Total num. of bins used: 20
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