[English] 日本語
Yorodumi- PDB-8q20: Crystal structure of Vanadium-dependent haloperoxidase R425D muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q20 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Vanadium-dependent haloperoxidase R425D mutant (A. marina) | ||||||
Components | Vanadium-dependent bromoperoxidase, putative | ||||||
Keywords | OXIDOREDUCTASE / Vanadium / Enzyme Catalysis / Peroxidase / Halogenation / Mutant | ||||||
Function / homology | Bromoperoxidase/chloroperoxidase C-terminal / : / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / peroxidase activity / PHOSPHATE ION / Vanadium-dependent bromoperoxidase, putative Function and homology information | ||||||
Biological species | Acaryochloris marina (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Zeides, P. / Bellmannn-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schroeder, C.T. / Groll, M. / Gulder, T. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: to be published Title: Unraveling the Molecular Basis of Substrate Specificity and Halogen Activation in Vanadium-Dependent Haloperoxidases Authors: Zeides, P. / Bellmannn-Sickert, K. / Zhang, R. / Seel, C.J. / Most, V. / Schroeder, C.T. / Groll, M. / Gulder, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8q20.cif.gz | 254.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8q20.ent.gz | 207.7 KB | Display | PDB format |
PDBx/mmJSON format | 8q20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q20_validation.pdf.gz | 699.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8q20_full_validation.pdf.gz | 703.6 KB | Display | |
Data in XML | 8q20_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 8q20_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/8q20 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/8q20 | HTTPS FTP |
-Related structure data
Related structure data | 8q21C 8q22C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 12||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 73068.539 Da / Num. of mol.: 1 / Mutation: R452D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acaryochloris marina (bacteria) / Gene: AM1_4975 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0C4R0 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-SO4 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.18 Å3/Da / Density % sol: 70.58 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M TRIS, 1.25 M Ammoniumdihydrogenphosphate, 0.5 mM potassium vanadate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 15830 / % possible obs: 96.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 5 % / Rmerge(I) obs: 0.632 / Num. unique obs: 1244 / % possible all: 96.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.926 / SU B: 54.558 / SU ML: 0.361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 160.04 Å2 / Biso mean: 96.498 Å2 / Biso min: 81.59 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 19.9442 Å / Origin y: 4.7943 Å / Origin z: 44.8523 Å
|