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- PDB-4z6z: 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: 4z6z | |||||||||
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Title | Structure of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-sulfonyl catechol at 1.52 Ang resolution | |||||||||
![]() | Homoprotocatechuate 2,3-dioxygenase | |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kovaleva, E.G. / Lipscomb, J.D. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200. Authors: Kovaleva, E.G. / Rogers, M.S. / 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 | ![]() | 651.4 KB | Display | ![]() |
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PDB format | ![]() | 535.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4z6lC ![]() 4z6mC ![]() 4z6nC ![]() 4z6oC ![]() 4z6pC ![]() 4z6qC ![]() 4z6rC ![]() 4z6sC ![]() 4z6tC ![]() 4z6uC ![]() 4z6vC ![]() 4z6wC ![]() 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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 1394 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/4SX.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MPO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/4SX.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-P6G / ![]() #4: Chemical | ChemComp-CL / ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-CA / | #7: Chemical | #8: Chemical | ChemComp-PG4 / | ![]() #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG6000, 0.1M calcium chloride, 0.1M MOPS |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→29.72 Å / Num. all: 239601 / Num. obs: 239601 / % possible obs: 97.5 % / Redundancy: 4.6 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.077 / Rsym value: 0.068 / Net I/av σ(I): 8.667 / Net I/σ(I): 12 / Num. measured all: 1094337 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3OJT Resolution: 1.52→29.51 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.1484 / WRfactor Rwork: 0.1106 / FOM work R set: 0.8895 / SU B: 3.01 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0666 / SU Rfree: 0.0609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.061 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.43 Å2 / Biso mean: 20.167 Å2 / Biso min: 7.18 Å2
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Refinement step | Cycle: final / Resolution: 1.52→29.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.559 Å / Total num. of bins used: 20
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