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- PDB-7qwi: Vanadate complex of the vanadium-dependent bromoperoxidase from C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qwi | ||||||
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Title | Vanadate complex of the vanadium-dependent bromoperoxidase from Corallina pilulifera | ||||||
![]() | Vanadium-dependent bromoperoxidase | ||||||
![]() | OXIDOREDUCTASE / Vanadium protein / halogen binding / haloperoxidase. | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Isupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: R396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera Authors: Isupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 573.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 115.7 KB | Display | |
Data in CIF | ![]() | 174.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qvwC ![]() 7qw3C ![]() 7qyyC ![]() 1up8S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 2 - 598 / Label seq-ID: 2 - 598
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 65614.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 3041 molecules ![](data/chem/img/VO4.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/144.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/144.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-VO4 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-BR / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-144 / #7: Chemical | ChemComp-PEG / #8: Chemical | ChemComp-EDO / #9: Chemical | ChemComp-PGE / #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50 mM Tris-H2SO4, pH 6.8, 0.4M KBr, 1mM Na3VO4, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→14.965 Å / Num. obs: 142571 / % possible obs: 96.4 % / Redundancy: 4.9 % / CC1/2: 0.977 / Rsym value: 0.155 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.15→2.19 Å / Num. unique obs: 2680 / CC1/2: 0.809 / Rsym value: 0.502 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1up8 Resolution: 2.15→14.965 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.177 / WRfactor Rwork: 0.131 / SU B: 4.775 / SU ML: 0.122 / Average fsc free: 0.9389 / Average fsc work: 0.9526 / Cross valid method: FREE R-VALUE / ESU R: 0.22 / ESU R Free: 0.173 / Details: Hydrogens have not been used
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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 PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.248 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→14.965 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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