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- PDB-4ghh: Structure of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ghh | ||||||
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Title | Structure of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol at 1.55 Ang resolution | ||||||
![]() | Homoprotocatechuate 2,3-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / Dioxygenase / oxygen activation / Fe(II) / 2-His-1-carboxylate facial triad / homoprotocatechuate / 4-nitrocatechol / oxy complex | ||||||
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 | ![]() | 656.2 KB | Display | ![]() |
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PDB format | ![]() | 542.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 67.5 KB | Display | |
Data in CIF | ![]() | 102.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ghcC ![]() 4ghdC ![]() 4gheC ![]() 4ghfC ![]() 4ghgC ![]() 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 on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 41755.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q45135, 3,4-dihydroxyphenylacetate 2,3-dioxygenase |
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-Non-polymers , 8 types, 1612 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/4NC.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/4NC.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-P6G / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-PG4 / | #7: Chemical | #8: Chemical | ChemComp-PEG / | #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: 48.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol for 1.5 hours in anaerobic glovebox atmosphere prior to cryo-cooling in ...Details: 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol for 1.5 hours in anaerobic glovebox atmosphere prior to cryo-cooling in liquid nitrogen., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→48.1 Å / Num. all: 231042 / Num. obs: 231042 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2 / Num. unique all: 33407 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3OJT Resolution: 1.55→47.83 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.777 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.065 / 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: 19.231 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→47.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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