[English] 日本語
Yorodumi- PDB-4whp: Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4whp | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Resting Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5 | |||||||||
Components |
| |||||||||
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: 1.541 Å | |||||||||
Authors | Knoot, C.J. / Lipscomb, J.D. | |||||||||
Funding support | United States, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4whp.cif.gz | 560.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4whp.ent.gz | 459.5 KB | Display | PDB format |
PDBx/mmJSON format | 4whp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4whp ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4whp | HTTPS FTP |
---|
-Related structure data
Related structure data | 4whoC 4whqC 4whrC 4whsC 3t63S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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 |
---|
-Protocatechuate 3,4-dioxygenase beta ... , 2 types, 3 molecules FDB
#2: Protein | Mass: 26696.287 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: 26712.287 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 |
---|
-Non-polymers , 5 types, 1124 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-BCT / | #7: Chemical | ChemComp-BME / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.26 % |
---|---|
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 MES pH 6.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 1.54→50 Å / Num. obs: 206314 / % possible obs: 93.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.061 / Rrim(I) all: 0.139 / Χ2: 4.061 / Net I/av σ(I): 29.661 / Net I/σ(I): 12.1 / Num. measured all: 1026896 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T63 Resolution: 1.541→39.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1696 / WRfactor Rwork: 0.1404 / FOM work R set: 0.9218 / SU B: 1.928 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0798 / SU Rfree: 0.0671 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 75.16 Å2 / Biso mean: 21.072 Å2 / Biso min: 11.95 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.541→39.02 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.541→1.581 Å / Total num. of bins used: 20
|