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Yorodumi- PDB-4whr: Anhydride reaction intermediate trapped in Protocatechuate 3,4-di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4whr | |||||||||
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Title | Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5 | |||||||||
Components |
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Keywords | OXIDOREDUCTASE / dioxygen activation / non-heme iron / intradiol dioxygenase / aromatic ring cleavage / catalytic intermediates | |||||||||
Function / homology | Function and homology information protocatechuate 3,4-dioxygenase / protocatechuate 3,4-dioxygenase activity / 3,4-dihydroxybenzoate catabolic process / beta-ketoadipate pathway / ferric iron binding Similarity search - Function | |||||||||
Biological species | Pseudomonas putida (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||
Authors | Knoot, C.J. / Lipscomb, J.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase. Authors: Knoot, C.J. / Purpero, V.M. / Lipscomb, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4whr.cif.gz | 567.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4whr.ent.gz | 465.9 KB | Display | PDB format |
PDBx/mmJSON format | 4whr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4whr ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4whr | HTTPS FTP |
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-Related structure data
Related structure data | 4whoC 4whpC 4whqC 4whsC 3t63S 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
-Protein , 1 types, 3 molecules AEC
#1: Protein | Mass: 22278.812 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaG / Plasmid: pCE120K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00436, protocatechuate 3,4-dioxygenase |
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-Protocatechuate 3,4-dioxygenase beta ... , 2 types, 3 molecules DBF
#2: Protein | Mass: 26712.287 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE120K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00437, protocatechuate 3,4-dioxygenase #3: Protein | | Mass: 26728.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE120K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00437, protocatechuate 3,4-dioxygenase |
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-Non-polymers , 7 types, 971 molecules
#4: Chemical | ChemComp-3N8 / #5: Chemical | ChemComp-BME / #6: Chemical | #7: Chemical | ChemComp-TRS / | #8: Chemical | ChemComp-3NJ / | #9: Chemical | ChemComp-CL / | #10: 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: 2.59 Å3/Da / Density % sol: 52.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM Tris-HCl pH 8.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→50 Å / Num. obs: 188155 / % possible obs: 91.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.076 / Rrim(I) all: 0.162 / Χ2: 4.025 / Net I/av σ(I): 23.986 / Net I/σ(I): 12.2 / Num. measured all: 756615 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T63 Resolution: 1.58→31.47 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.1879 / WRfactor Rwork: 0.1489 / FOM work R set: 0.8956 / SU B: 2.658 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0967 / SU Rfree: 0.0809 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.29 Å2 / Biso mean: 24.54 Å2 / Biso min: 12.21 Å2
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Refinement step | Cycle: final / Resolution: 1.58→31.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.58→1.623 Å / Total num. of bins used: 20
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