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- PDB-4ghf: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ghf | ||||||
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Title | Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution | ||||||
![]() | Homoprotocatechuate 2,3-dioxygenase | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kovaleva, E.G. / Lipscomb, J.D. | ||||||
![]() | ![]() Title: Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation. Authors: Kovaleva, E.G. / 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 | ![]() | 604.4 KB | Display | ![]() |
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PDB format | ![]() | 499.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ghcC ![]() 4ghdC ![]() 4gheC ![]() 4ghgC ![]() 4ghhC ![]() 3ojtS 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41739.320 Da / Num. of mol.: 4 / Mutation: Y257F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q45135, ![]() |
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-Non-polymers , 8 types, 1190 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/4NC.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4NC.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | #4: Chemical | ChemComp-P6G / ![]() #5: Chemical | ChemComp-CL / ![]() #6: Chemical | ChemComp-CA / | #7: Chemical | ![]() #8: Chemical | ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol under aerobic conditions for 1hr prior to cryo-cooling in liquid nitrogen. , ...Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol under aerobic conditions for 1hr prior to cryo-cooling in liquid nitrogen. , pH pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.67→96.11 Å / Num. all: 184533 / Num. obs: 184533 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3OJT Resolution: 1.67→89.04 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.567 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.656 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→89.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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