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Yorodumi- PDB-9f95: Complex of phenazine biosynthesis enzyme PhzF with 2-amino-3-hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9f95 | ||||||
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Title | Complex of phenazine biosynthesis enzyme PhzF with 2-amino-3-hydroxy-5-(3-hydroxyphenyl)benzoic acid | ||||||
Components | Trans-2,3-dihydro-3-hydroxyanthranilate isomerase | ||||||
Keywords | ISOMERASE / Inhibitor / Complex / Phenazine biosynthesis / Pyocyanin | ||||||
Function / homology | trans-2,3-dihydro-3-hydroxyanthranilate isomerase / trans-2,3-dihydro-3-hydroxy-anthranilate isomerase activity / Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / phenazine biosynthetic process / cytoplasm / : / Trans-2,3-dihydro-3-hydroxyanthranilate isomerase Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Baumgarten, J. / Schneider, P. / Blankenfeldt, W. / Kunick, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Chemmedchem / Year: 2024 Title: Substrate-Based Ligand Design for Phenazine Biosynthesis Enzyme PhzF. Authors: Baumgarten, J. / Schneider, P. / Thiemann, M. / Zimmermann, M. / Diederich, C. / Blankenfeldt, W. / Kunick, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f95.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f95.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9f95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f95_validation.pdf.gz | 743.2 KB | Display | wwPDB validaton report |
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Full document | 9f95_full_validation.pdf.gz | 743.2 KB | Display | |
Data in XML | 9f95_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 9f95_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/9f95 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/9f95 | HTTPS FTP |
-Related structure data
Related structure data | 9f92C 9f93C 9f94C 9f96C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 32256.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: 2-79 / Gene: phzF / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q51792, trans-2,3-dihydro-3-hydroxyanthranilate isomerase |
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#2: Chemical | ChemComp-A1IAU / Mass: 245.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO4 / Feature type: SUBJECT OF INVESTIGATION |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 2-amino-3-hydroxy-5-(3-hydroxyphenyl)benzoic acid (42 mM), propan-2-ol (19%), glycerol (5%), PEG 4000 (19%), sodium citrate (pH 5.6, 95 mM) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→48.72 Å / Num. obs: 50874 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.015 / Rrim(I) all: 0.066 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7307 / CC1/2: 0.892 / Rpim(I) all: 0.226 / Rrim(I) all: 0.997 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→48.72 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→48.72 Å
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Refine LS restraints |
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LS refinement shell |
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