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- PDB-8a91: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8a91 | ||||||
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Title | Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment | ||||||
![]() | Cytochrome P450 protein | ||||||
![]() | OXIDOREDUCTASE / CYPX / CYP134 / staphylococcus / fragment / heme / cyclic leucine / CLL / diketopiperazine / iron | ||||||
Function / homology | ![]() Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Snee, M. / Katariya, M. / Levy, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment Authors: Snee, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.4 KB | Display | ![]() |
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PDB format | ![]() | 150 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8a8lC ![]() 8ae8C ![]() 7ow9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() ![]() References: UniProt: A0A380DQV1, pulcherriminic acid synthase | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-LC9 / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.15M Lithium sulfate, 0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.8, 20% 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→55.38 Å / Num. obs: 40202 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 30.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.115 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 13.4 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2451 / CC1/2: 0.793 / Rpim(I) all: 0.785 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7OW9 Resolution: 1.85→55.38 Å / SU ML: 0.2587 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2682 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: 45.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→55.38 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: -17.7483680921 Å / Origin y: -23.356345485 Å / Origin z: -6.03811596646 Å
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Refinement TLS group | Selection details: all |