[English] 日本語
Yorodumi- PDB-1dlt: STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dlt | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL | ||||||
Components | CATECHOL 1,2-DIOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / METALLOENZYME / DIOXYGENASE / AROMATIC HYDROCARBON DEGREDATION / ALPHA/BETA MOTIF / 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: 1.9 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dlt.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dlt.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 1dlt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/1dlt ftp://data.pdbj.org/pub/pdb/validation_reports/dl/1dlt | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly of the molecule is a homodimer consisting of subunit A and subunit B related by a non-crystallographic two-fold |
-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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.33 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 58895 / Num. obs: 54078 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.89→1.95 Å / Redundancy: 1.75 % / Rmerge(I) obs: 0.279 / Num. unique all: 8580 / % possible all: 84.9 |
Reflection | *PLUS Num. obs: 61083 / % possible obs: 96.4 % / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 85 % / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.187 / Rfactor Rfree: 0.227 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.7 |