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Yorodumi- PDB-3h76: Crystal structure of PqsD, a key enzyme in Pseudomonas aeruginosa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h76 | ||||||
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Title | Crystal structure of PqsD, a key enzyme in Pseudomonas aeruginosa quinolone signal biosynthesis pathway | ||||||
Components | PQS biosynthetic enzyme | ||||||
Keywords | TRANSFERASE / PqsD / PQS / ANTHRANILOYL-CoA / ANTHRANILIC ACID | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 3h76.cif.gz | 263.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h76.ent.gz | 212.2 KB | Display | PDB format |
PDBx/mmJSON format | 3h76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h76_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 3h76_full_validation.pdf.gz | 455.2 KB | Display | |
Data in XML | 3h76_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 3h76_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h76 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h76 | HTTPS FTP |
-Related structure data
Related structure data | 3h77C 3h78C 1hn9S 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
#1: Protein | Mass: 38744.227 Da / Num. of mol.: 2 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: 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: 1.94 Å3/Da / Density % sol: 36.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.16 M MgCl2, 0.08M Tris-HCl pH 8.5, 24% PEG 4000, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27 Å / Num. obs: 49952 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.07 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HN9 Resolution: 1.8→25.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.617 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.17 / 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: 34.725 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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