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- PDB-3lmx: Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficien... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3lmx | ||||||
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Title | Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis | ||||||
![]() | (Protocatechuate 3,4-dioxygenase ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / Protocatechuate / dihydroxybenzoic acid / ES complex / dioxygenase / non-heme / iron dependent | ||||||
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. / Shi, K. | ||||||
![]() | ![]() Title: Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis Authors: Purpero, V.M. / Lipscomb, J.D. / Ohlendorf, D.H. / Shi, K. / Dolbeare, K.B. / Brown, C.K. / Burk, 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 | ![]() | 286.3 KB | Display | ![]() |
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PDB format | ![]() | 231.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 535.7 KB | Display | ![]() |
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Full document | ![]() | 549.8 KB | Display | |
Data in XML | ![]() | 55.8 KB | Display | |
Data in CIF | ![]() | 78.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 26671.260 Da / Num. of mol.: 3 / Mutation: Y447H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00437, protocatechuate 3,4-dioxygenase |
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-Non-polymers , 7 types, 659 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/DHB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/DHB.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-BME / #6: Chemical | ChemComp-CL / #7: Chemical | #8: Chemical | ChemComp-DHB / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.14 % |
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Crystal grow | Temperature: 277 K / pH: 8.5 Details: 1.5-1.8 M ammonium sulfate; 40-60 mM TRIS-Hcl buffer; 5 mM BME, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2007 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→23.076 Å / Num. all: 76918 / Num. obs: 76802 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 32.23 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.21 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.49 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 33.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→22.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.25 Å / Total num. of bins used: 20
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