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Open data
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Basic information
Entry | Database: PDB / ID: 3vef | ||||||
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Title | Rhodococcus jostii RHA1 DypB N246H variant in complex with heme | ||||||
![]() | DypB | ||||||
![]() | OXIDOREDUCTASE / peroxidase / lignan / Dyp | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grigg, J.C. / Singh, R. / Armstrong, Z. / Eltis, L.D. / Murphy, M.E.P. | ||||||
![]() | ![]() Title: Distal heme pocket residues of B-type dye-decolorizing peroxidase: arginine but not aspartate is essential for peroxidase activity. Authors: Singh, R. / Grigg, J.C. / Armstrong, Z. / Murphy, M.E. / Eltis, L.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 | ![]() | 200.1 KB | Display | ![]() |
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PDB format | ![]() | 158 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 40.4 KB | Display | |
Data in CIF | ![]() | 55.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vecC ![]() 3vedC ![]() 3veeC ![]() 3vegC ![]() 3qnrS 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
#1: Protein | Mass: 37561.609 Da / Num. of mol.: 3 / Mutation: N246H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q0SE24, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M sodium acetate trihydrate, 3 M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 15, 2010 Details: Collimating Mirror with two stripes (Si, Rh/Pt), Toroidal Focusing Mirror (Rh/Pt) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: KOHZU double crystal monochromator (DCM), featuring indirectly water-cooled first crystal and flat, long second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→45 Å / Num. obs: 47453 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.074 / Χ2: 0.993 / Net I/σ(I): 14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3QNR Resolution: 2.64→45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.685 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.99 Å2 / Biso mean: 51.2625 Å2 / Biso min: 9.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.708 Å / Total num. of bins used: 20
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