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Yorodumi- PDB-1dmh: STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dmh | ||||||
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Title | STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND 4-METHYLCATECHOL | ||||||
Components | CATECHOL 1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / DIOXYGENASE / AROMATIC HYDROCARBON DEGRADATION / ALPHA/BETA FOLD / METALLOENZYME / SUBSTRATE | ||||||
Function / homology | Function and homology information catechol-containing compound catabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / beta-ketoadipate pathway / ferric iron binding Similarity search - Function | ||||||
Biological species | Acinetobacter sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Vetting, M.W. / Ohlendorf, D.H. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker. Authors: Vetting, M.W. / Ohlendorf, D.H. #1: Journal: J.Bacteriol. / Year: 1988 Title: DNA Sequence of the Acinetobacter calcoaceticus Catechol 1,2-dioxygenase I Structural Gene catA: Evidence for Evolutionary Divergence of Intradiol Dioxygenases by Aquisition of DNA Sequence Repetitions Authors: Neidle, E.L. / Harnett, C. / Bonitz, S. / Ornston, L.N. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Structure of Protocatechuate 3,4-dioxygenase from Psuedomonas aeruginosa at 2.15 A Resolution Authors: Ohlendorf, D.H. / Orville, A.M. / Lipscomb, J.D. #3: Journal: Biochemistry / Year: 1997 Title: Crystal Structures of Substrate and Substrate Analog Complexes of Protocatechuate 3,4-dioxygenase: Endogenous Fe+3 Ligand Displacement in Response to Substrate Binding. Authors: Orville, A.M. / Lipscomb, J.D. / Ohlendorf, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dmh.cif.gz | 139.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dmh.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dmh_validation.pdf.gz | 963.2 KB | Display | wwPDB validaton report |
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Full document | 1dmh_full_validation.pdf.gz | 980.8 KB | Display | |
Data in XML | 1dmh_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 1dmh_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dmh ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dmh | 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: 34384.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter sp. (bacteria) / Strain: ADP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07773, catechol 1,2-dioxygenase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.83 Å3/Da / Density % sol: 56.58 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10-15% PEG5000, 100MM TRIS-HCL, PH 7.5, .2M MGACETATE, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||
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 2, 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: 1.7→20 Å / Num. all: 70971 / Num. obs: 65553 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.68→1.75 Å / Redundancy: 1.48 % / Rmerge(I) obs: 0.294 / % possible all: 59.7 |
Reflection | *PLUS Num. obs: 87127 / % possible obs: 93 % / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 60 % / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Resolution: 1.7→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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