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- PDB-1dlt: STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dlt | ||||||
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Title | STRUCTURE OF CATECHOL 1,2-DIOXYGENASE FROM ACINETOBACTER SP. ADP1 WITH BOUND CATECHOL | ||||||
![]() | CATECHOL 1,2-DIOXYGENASE | ||||||
![]() | OXIDOREDUCTASE / METALLOENZYME / DIOXYGENASE / AROMATIC HYDROCARBON DEGREDATION / ALPHA/BETA MOTIF / SUBSTRATE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Vetting, M.W. / Ohlendorf, D.H. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.9 KB | Display | ![]() |
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PDB format | ![]() | 108.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 895.9 KB | Display | ![]() |
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Full document | ![]() | 913.5 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly of the molecule is a homodimer consisting of subunit A and subunit B related by a non-crystallographic two-fold |
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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.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.33 % | |||||||||||||||||||||||||
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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: ![]() |
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 |
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Processing
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Refinement | Resolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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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 |