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Yorodumi- PDB-3lkt: Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficien... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lkt | ||||||
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Title | Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis | ||||||
Components | (Protocatechuate 3,4-dioxygenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Protocatechuate / dioxygenase / non-heme / Y447H / iron-dependent / Aromatic hydrocarbons catabolism / Iron / Metal-binding | ||||||
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: 1.65 Å | ||||||
Authors | Lipscomb, J.D. / Purpero, V.M. | ||||||
Citation | Journal: To be Published 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. / Burk, D. / Dolbeare, K.B. / Brown, K.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lkt.cif.gz | 587.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lkt.ent.gz | 477 KB | Display | PDB format |
PDBx/mmJSON format | 3lkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/3lkt ftp://data.pdbj.org/pub/pdb/validation_reports/lk/3lkt | HTTPS FTP |
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-Related 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
-Protocatechuate 3,4-dioxygenase ... , 2 types, 12 molecules ABCDEFMNOPQR
#1: Protein | Mass: 22278.812 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaG / Plasmid: pCE025 / 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.: 6 / Mutation: Y447H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Plasmid: pCE025 / 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, 2819 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BME / #5: Chemical | ChemComp-TRS / #6: Chemical | ChemComp-FE / #7: Chemical | ChemComp-CL / #8: Chemical | #9: 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: 2.58 Å3/Da / Density % sol: 52.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5-1.8 M ammonium sulfate, 40-60 mM TRIS-HCl buffer, pH 8.5, 5 mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 23, 2009 / Details: vertical focusing mirror |
Radiation | Monochromator: Sagitally focusing crystal and a double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 357899 / Num. obs: 351447 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.9 / % possible all: 97.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 33.32 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PHASER generated pdb Resolution: 1.65→29.57 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.366 / SU ML: 0.048 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.377 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→29.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.647→1.69 Å / Total num. of bins used: 20
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