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Yorodumi- PDB-3t67: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleava... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t67 | ||||||
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Title | Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase | ||||||
Components | (Protocatechuate 3,4-dioxygenase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / non-heme ironIII dependent intradiol dioxygenase | ||||||
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: 1.67 Å | ||||||
Authors | Purpero, V.M. / Lipscomb, J.D. | ||||||
Citation | Journal: To be Published Title: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase Authors: 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 | 3t67.cif.gz | 287.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t67.ent.gz | 230.1 KB | Display | PDB format |
PDBx/mmJSON format | 3t67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t67 ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t67 | HTTPS FTP |
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-Related structure data
Related structure data | 3mflC 3mi1C 3mi5C 3mv4C 3mv6C 3t63C 2pcdS 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
-Protocatechuate 3,4-dioxygenase ... , 2 types, 6 molecules ABCMNO
#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 #2: Protein | Mass: 26696.287 Da / Num. of mol.: 3 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 , 5 types, 953 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CAQ / #6: Chemical | #7: 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: 52.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5-1.8 M ammonium sulfate, 2-5 mM BME, 40-60 mM Tris-HCl, pH 7.5, 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: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 16, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Sagitally focused double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.67→50 Å / Num. all: 173935 / Num. obs: 172718 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.029 / Net I/σ(I): 14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PCD CHAINS A/M, B/N, C/O Resolution: 1.67→30.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1841 / WRfactor Rwork: 0.1605 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8905 / SU B: 1.527 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0877 / SU Rfree: 0.0855 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.088 / ESU R Free: 0.085 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.91 Å2 / Biso mean: 21.0206 Å2 / Biso min: 12.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→30.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.672→1.716 Å / Total num. of bins used: 20
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