+Open data
-Basic information
Entry | Database: PDB / ID: 1ykk | ||||||
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Title | Protocatechuate 3,4-Dioxygenase Y408C Mutant | ||||||
Components |
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Keywords | OXIDOREDUCTASE / 3 / 4-PCD / catechol / protocatechuate / 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 / FOURIER SYNTHESIS / Resolution: 2.06 Å | ||||||
Authors | Brown, C.K. / Ohlendorf, D.H. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Roles of the equatorial tyrosyl iron ligand of protocatechuate 3,4-dioxygenase in catalysis Authors: Valley, M.P. / Brown, C.K. / Burk, D.L. / Vetting, M.W. / Ohlendorf, D.H. / 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 | 1ykk.cif.gz | 521 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ykk.ent.gz | 429.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ykk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ykk_validation.pdf.gz | 514.2 KB | Display | wwPDB validaton report |
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Full document | 1ykk_full_validation.pdf.gz | 535.9 KB | Display | |
Data in XML | 1ykk_validation.xml.gz | 95.2 KB | Display | |
Data in CIF | 1ykk_validation.cif.gz | 133.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/1ykk ftp://data.pdbj.org/pub/pdb/validation_reports/yk/1ykk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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 / Production host: Escherichia coli (E. coli) References: UniProt: P00436, protocatechuate 3,4-dioxygenase #2: Protein | Mass: 26712.373 Da / Num. of mol.: 6 / Mutation: Y108C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: pcaH / Production host: Escherichia coli (E. coli) References: UniProt: P00437, protocatechuate 3,4-dioxygenase #3: Chemical | ChemComp-FE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.66 % |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 19.2 Å2 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3,4 PCD Resolution: 2.06→26.09 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4441456.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 11.5877 Å2 / ksol: 0.297246 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.06→26.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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