[English] 日本語
Yorodumi- PDB-8rgw: Serial synchrotron in plate room temperature structure of Dye Typ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rgw | ||||||
---|---|---|---|---|---|---|---|
Title | Serial synchrotron in plate room temperature structure of Dye Type Peroxidase Aa, 12 drops merged | ||||||
Components | Deferrochelatase | ||||||
Keywords | OXIDOREDUCTASE / serial synchrotron crystallography / heme peroxidase / metalloproteins | ||||||
Function / homology | Function and homology information iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / lyase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces lividans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Thompson, A.J. / Hough, M.A. / Williams, L.J. / Worrall, J.A.R. / Sanchez-Weatherby, J. / Mikolajek, H. / Sandy, J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2024 Title: Efficient in situ screening of and data collection from microcrystals in crystallization plates. Authors: Thompson, A.J. / Sanchez-Weatherby, J. / Williams, L.J. / Mikolajek, H. / Sandy, J. / Worrall, J.A.R. / Hough, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8rgw.cif.gz | 175.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8rgw.ent.gz | 124.1 KB | Display | PDB format |
PDBx/mmJSON format | 8rgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/8rgw ftp://data.pdbj.org/pub/pdb/validation_reports/rg/8rgw | HTTPS FTP |
---|
-Related structure data
Related structure data | 8rgeC 8rgsC 8rgyC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40240.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: SLI_2602 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A7U9DT46 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.86 % |
---|---|
Crystal grow | Temperature: 291 K / Method: batch mode / pH: 7 Details: 1:3 v/v ratio of 10 mg/ml protein in 20 mM sodium phosphate, 150 mM NaCl, pH 7.0 and a mother liquor solution (12% v/v PEG 3350, 100 mM HEPES, pH 7.0) |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.775 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Oct 4, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.775 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→69.73 Å / Num. obs: 56729 / % possible obs: 99.73 % / Redundancy: 48 % / Biso Wilson estimate: 20.43 Å2 / CC1/2: 0.958 / R split: 0.203 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.88→1.947 Å / Num. unique obs: 5631 / CC1/2: 0.302 / R split: 1.061 |
Serial crystallography sample delivery | Description: In Plate / Method: fixed target |
Serial crystallography sample delivery fixed target | Description: Mitegen in situ-1 plate |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→69.73 Å / SU ML: 0.244 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8052 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→69.73 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|