+Open data
-Basic information
Entry | Database: PDB / ID: 3qns | ||||||
---|---|---|---|---|---|---|---|
Title | DyPB from Rhodococcus jostii RHA1, crystal form 2 | ||||||
Components | DyP Peroxidase | ||||||
Keywords | OXIDOREDUCTASE / peroxidase / lignan / heme / DyP / enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodococcus jostii RHA1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Grigg, J.C. / Roberts, J.N. / Singh, R. / Eltis, L.D. / Murphy, M.E.P. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1. Authors: Roberts, J.N. / Singh, R. / Grigg, J.C. / Murphy, M.E. / Bugg, T.D. / Eltis, L.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qns.cif.gz | 162.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qns.ent.gz | 127.3 KB | Display | PDB format |
PDBx/mmJSON format | 3qns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/3qns ftp://data.pdbj.org/pub/pdb/validation_reports/qn/3qns | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 37537.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Strain: RHA1 / Gene: DyPB, RHA1_ro02407 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0SE24 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 66.98 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.26 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2010 / Details: Rh coated flat mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→93.972 Å / Num. all: 108171 / Num. obs: 108171 / % possible obs: 98.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→33.93 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.09 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 180.43 Å2 / Biso mean: 17.2251 Å2 / Biso min: 6.15 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→33.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
|