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Yorodumi- PDB-1eob: CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eob | ||||||
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Title | CRYSTAL STRUCTURE OF ACINETOBACTER SP. ADP1 PROTOCATECHUATE 3,4-DIOXYGENASE IN COMPLEX WITH 3,4-DIHYDROXYBENZOATE | ||||||
Components |
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Keywords | OXIDOREDUCTASE / beta-sandwich / mixed alpha/beta structure / dioxygenase / biodegradation | ||||||
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 | Acinetobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Vetting, M.W. / D'Argenio, D.A. / Ornston, L.N. / Ohlendorf, D.H. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase. Authors: Vetting, M.W. / D'Argenio, D.A. / Ornston, L.N. / Ohlendorf, D.H. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-ray Analysis of Protocatechuate 3,4-dioxygenase from Acinetobacter calcoaceticus Authors: Vetting, M.W. / Earhart, C.A. / Ohlendorf, D.H. #2: Journal: J.Bacteriol. / Year: 1999 Title: Substitution, Insertion, Deletion, Suppression, and Altered Substrate Specificity in Functional Protocatechuate 3,4-dioxygenases. Authors: D'Argenio, D.A. / Vetting, M.W. / Ohlendorf, D.H. / Ornston, L.N. #3: Journal: Biochemistry / Year: 1997 Title: Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-dioxygenase: Endogenous Fe3+ Ligand Displacement in Response to Substrate binding. Authors: Orville, A.M. / Lipscomb, J.D. / Ohlendorf, D.H. #4: Journal: J.Mol.Biol. / Year: 1994 Title: Structure of Protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 A resolution Authors: Ohlendorf, D.H. / Orville, A.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 | 1eob.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eob.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 1eob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/1eob ftp://data.pdbj.org/pub/pdb/validation_reports/eo/1eob | 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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Details | The biological assembly is a dodecamer (AB) X 12 constructed from the 23(T) symmetry of the space group acting on the A and B subunits in the assymetric unit. |
-Components
#1: Protein | Mass: 23508.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Description: CLONED AND OVEREXPRESSED IN E.COLI / Production host: Escherichia coli (E. coli) References: UniProt: P20371, protocatechuate 3,4-dioxygenase |
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#2: Protein | Mass: 27583.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Production host: Escherichia coli (E. coli) References: UniProt: P20372, protocatechuate 3,4-dioxygenase |
#3: Chemical | ChemComp-FE / |
#4: Chemical | ChemComp-DHB / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.88 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Tris-HCl pH 7.0, 2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K Crystals were soaked in 30mM PCA at pH 8.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 108614 / Num. obs: 25259 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.332 / % possible all: 86.4 |
Reflection shell | *PLUS % possible obs: 86.4 % / Mean I/σ(I) obs: 0.9 |
-Processing
Software |
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Refinement | Resolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.006 |