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Yorodumi- PDB-2pia: PHTHALATE DIOXYGENASE REDUCTASE: A MODULAR STRUCTURE FOR ELECTRON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pia | ||||||
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Title | PHTHALATE DIOXYGENASE REDUCTASE: A MODULAR STRUCTURE FOR ELECTRON TRANSFER FROM PYRIDINE NUCLEOTIDES TO [2FE-2S] | ||||||
Components | PHTHALATE DIOXYGENASE REDUCTASE | ||||||
Keywords | REDUCTASE | ||||||
Function / homology | Function and homology information Oxidoreductases / 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Burkholderia cepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Correll, C.C. / Batie, C.J. / Ballou, D.P. / Ludwig, M.L. | ||||||
Citation | Journal: Science / Year: 1992 Title: Phthalate dioxygenase reductase: a modular structure for electron transfer from pyridine nucleotides to [2Fe-2S]. Authors: Correll, C.C. / Batie, C.J. / Ballou, D.P. / Ludwig, M.L. #1: Journal: J.Biol.Chem. / Year: 1985 Title: Crystallographic Characterization of Phthalate Oxygenase Reductase, an Iron-Sulfur Flavoprotein from Pseudomonas Cepacia Authors: Correll, C.C. / Batie, C.J. / Ballou, D.P. / Ludwig, M.L. #2: Journal: Flavins and Flavoproteins / Year: 1991 Title: Structure Determination of an Iron-Sulfur Flavoprotein Authors: Correll, C.C. / Ludwig, M.L. #3: Journal: Chemistry and Biochemistry of Flavoenzymes / Year: 1991 Title: Phthalate Dioxygenase Reductase and Related Flavin-Iron-Sulfur Containing Electron Transferases Authors: Batie, C.J. / Ballou, D.P. / Correll, C.C. | ||||||
History |
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Remark 700 | SHEET ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON THE ALGORITHM OF KABSCH AND SANDER. ...SHEET ASSIGNMENTS OF SECONDARY STRUCTURE ARE BASED ON THE ALGORITHM OF KABSCH AND SANDER. EXCEPTIONS: STRANDS 3 AND 4 OF BETA SHEET 2 IN WHICH THE KABSCH AND SANDER ALGORITHM INDICATED BREAKS. THE CLOSED SHEET (BETA BARREL) IS INDICATED BY HAVING THE FIRST AND LAST STRANDS IDENTICAL -THE FIRST STRAND APPEARS FIRST AND LAST. THE FMN HYDROGEN BONDS BETWEEN STRANDS 3 AND 4 TO CLOSE THE BARREL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pia.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pia.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pia_validation.pdf.gz | 466.9 KB | Display | wwPDB validaton report |
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Full document | 2pia_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 2pia_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 2pia_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/2pia ftp://data.pdbj.org/pub/pdb/validation_reports/pi/2pia | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35579.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cepacia (bacteria) References: UniProt: P33164, Oxidoreductases; Acting on iron-sulfur proteins as donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-FES / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS DEDUCED FROM THE DNA SEQUENCE DETERMINED BY R. LIU AND G. ZYLSTRA, ABS. ANN. ...THE SEQUENCE IS DEDUCED FROM THE DNA SEQUENCE DETERMINED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
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Crystal grow | *PLUS Method: other / Details: Correll, C.C., (1985) J. Biol. Chem., 260, 14633. |
-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 23943 / % possible obs: 93 % / Rmerge(I) obs: 0.062 |
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-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refinement | *PLUS Rfactor obs: 0.186 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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