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- PDB-3t67: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleava... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t67 | ||||||
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Title | Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase | ||||||
![]() | (Protocatechuate 3,4-dioxygenase ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / non-heme ironIII dependent intradiol dioxygenase | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Purpero, V.M. / Lipscomb, J.D. | ||||||
![]() | ![]() Title: Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase Authors: Purpero, V.M. / Lipscomb, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 287.7 KB | Display | ![]() |
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PDB format | ![]() | 230.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 506.7 KB | Display | ![]() |
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Full document | ![]() | 520 KB | Display | |
Data in XML | ![]() | 57.1 KB | Display | |
Data in CIF | ![]() | 81.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mflC ![]() 3mi1C ![]() 3mi5C ![]() 3mv4C ![]() 3mv6C ![]() 3t63C ![]() 2pcdS C: citing same article ( S: Starting model for refinement |
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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
-Protocatechuate 3,4-dioxygenase ... , 2 types, 6 molecules ABCMNO
#1: Protein | Mass: 22278.812 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00436, protocatechuate 3,4-dioxygenase #2: Protein | Mass: 26696.287 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00437, protocatechuate 3,4-dioxygenase |
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-Non-polymers , 5 types, 953 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CAQ.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CAQ.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CAQ / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5-1.8 M ammonium sulfate, 2-5 mM BME, 40-60 mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 16, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Sagitally focused double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.67→50 Å / Num. all: 173935 / Num. obs: 172718 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.029 / Net I/σ(I): 14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PCD CHAINS A/M, B/N, C/O Resolution: 1.67→30.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1841 / WRfactor Rwork: 0.1605 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8905 / SU B: 1.527 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0877 / SU Rfree: 0.0855 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.91 Å2 / Biso mean: 21.0206 Å2 / Biso min: 12.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→30.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.672→1.716 Å / Total num. of bins used: 20
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