[English] 日本語
Yorodumi- PDB-3lxv: Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficien... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lxv | ||||||
---|---|---|---|---|---|---|---|
Title | Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis | ||||||
Components | (Protocatechuate 3,4-dioxygenase ...) x 2 | ||||||
Keywords | oxidoreductase/oxidoreductase / dioxygenase / non-heme / iron-dependent / aromatic metabolism / 4-nitrocatechol / inhibitor / oxidoreductase-oxidoreductase complex | ||||||
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 / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Purpero, V.M. / Lipscomb, J.D. | ||||||
Citation | Journal: To be Published / Year: 2010 Title: Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis Authors: Purpero, V.M. / Valley, M.P. / Ohlendorf, D.H. / Lipscomb, J.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3lxv.cif.gz | 298.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3lxv.ent.gz | 237.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/3lxv ftp://data.pdbj.org/pub/pdb/validation_reports/lx/3lxv | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | In solution 34PCD is a dodecamer of the dimer in asymmetric unit. |
-Components
-Protocatechuate 3,4-dioxygenase ... , 2 types, 6 molecules ABCMNO
#1: Protein | Mass: 22278.812 Da / Num. of mol.: 3 / Mutation: Y148H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaG / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P00436, protocatechuate 3,4-dioxygenase #2: Protein | Mass: 26671.260 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P00437, protocatechuate 3,4-dioxygenase |
---|
-Non-polymers , 9 types, 1105 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-BME / #6: Chemical | #7: Chemical | ChemComp-CO3 / #8: Chemical | #9: Chemical | ChemComp-4NC / #10: Chemical | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5-1.8 M AS in 40-60 mM TRIS-HCl buffer, with varying protein:mother liquor ratios. 15-30 mg/mL protein conc, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Feb 11, 2010 Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.01 Å / Num. all: 118927 / Num. obs: 118774 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 7.11 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.082 / Χ2: 0.95 / Net I/σ(I): 9.2 / Scaling rejects: 8525 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.61 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.5 / Num. measured all: 78298 / Num. unique all: 11764 / Χ2: 1.27 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→41.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.78 / SU B: 3.504 / SU ML: 0.103 / SU R Cruickshank DPI: 0.164 / SU Rfree: 0.154 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 3 / ESU R: 0.164 / ESU R Free: 0.154 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.33 Å2 / Biso mean: 32.477 Å2 / Biso min: 4.29 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→41.99 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|