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- PDB-2buq: Crystal Structure Of Wild-Type Protocatechuate 3,4-Dioxygenase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2buq | ||||||
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Title | Crystal Structure Of Wild-Type Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 in Complex with Catechol | ||||||
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![]() | OXIDOREDUCTASE / DIOXYGENASE / AROMATIC DEGRADATION / NON-HEME IRON / BETA- SANDWICH / MIXED ALPHA/BETA STRUCTURE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vetting, M.W. / Valley, M.P. / D'Argenio, D.A. / Ornston, L.N. / Lipscomb, J.D. / Ohlendorf, D.H. | ||||||
![]() | ![]() Title: Biophysical Analyses of Designed and Selected Mutants of Protocatechuate 3,4-Dioxygenase Authors: Brown, C.K. / Vetting, M.W. / Earhart, C.A. / Ohlendorf, D.H. #1: ![]() Title: Crystallographic Studies of Intradiol Dioxygenases Authors: Vetting, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 82.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2bumC ![]() 2burC ![]() 2butC ![]() 2buvC ![]() 1eo2S S: Starting model for refinement C: citing same article ( |
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Similar 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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Components on special symmetry positions |
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Details | THE PHYSIOLOGICAL STATE OF THE MOLECULE IS A (AB)12DODECAMER.FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 |
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Components
#1: Protein | Mass: 23508.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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.) ![]() ![]() ![]() References: UniProt: P20372, protocatechuate 3,4-dioxygenase | ||||
#3: Chemical | ChemComp-FE / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | RESIDUES ARE NUMBERED TO CORRELATE WITH RESIDUE NUMBERING OF 3,4-PCD FROM PSEUDOMONAS PUTIDA ...RESIDUES ARE NUMBERED TO CORRELATE WITH RESIDUE NUMBERING OF 3,4-PCD FROM PSEUDOMONA | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % Description: CRYSTAL WAS SOAKED IN 2.0 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5, 30 MM CATECHOL WITHIN AN ANEROBIC ENVIRONMENT PRIOR TO DATA COLLECTION. |
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Crystal grow | pH: 8.5 Details: 1.8 M AMMONIUM SULFATE, 100 MM TRIS-MALEATE PH 7.5, 0.08% PEG4000 PROTEIN AT 20 MG/ML |
-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MAXFLUX OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 46389 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.3 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EO2 Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 27.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.254 |