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Yorodumi- PDB-8abo: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8abo | ||||||
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Title | Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a fragment | ||||||
Components | CYPX | ||||||
Keywords | OXIDOREDUCTASE / CYP / CYPX / Staphylococcus aureus / CLL / Pulcherremin / P450 | ||||||
Function / homology | 4-PHENYL-1H-IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / NITRATE ION Function and homology information | ||||||
Biological species | Staphylococcus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Snee, M. / Katariya, M. / Levy, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a fragment Authors: Snee, M. / Katariya, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8abo.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8abo.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 8abo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8abo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8abo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8abo_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 8abo_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/8abo ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abo | HTTPS FTP |
-Related structure data
Related structure data | 8adrC 7pq1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45974.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus (bacteria) / Plasmid: pET47b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 | ||||
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#2: Chemical | ChemComp-231 / | ||||
#3: Chemical | ChemComp-HEM / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Ammonium nitrate, 0.1M Bis-Tris propane pH 8.5, 18% v/v PEG smear High Temp details: 4C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→53.68 Å / Num. obs: 30618 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 34.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.02 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2129 / CC1/2: 0.967 / Rpim(I) all: 0.213 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PQ1 Resolution: 1.97→53.68 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.0004 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→53.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -16.5499592451 Å / Origin y: -22.2090157304 Å / Origin z: -5.93775278281 Å
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Refinement TLS group | Selection details: all |