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Yorodumi- PDB-8abr: Crystal structure of CYP109A2 from Bacillus megaterium bound with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8abr | |||||||||
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Title | Crystal structure of CYP109A2 from Bacillus megaterium bound with putative ligands hexanoic acid and octanoic acid | |||||||||
Components | Cytochrome P450 | |||||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 monooxygenase / Complex / Fatty acid / Steroid hydroxylation | |||||||||
Function / homology | Function and homology information 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 | Priestia megaterium DSM 319 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Jozwik, I.K. / Rozeboom, H.J. / Thunnissen, A.-M.W.H. | |||||||||
Funding support | European Union, 2items
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Citation | Journal: Febs J. / Year: 2023 Title: Regio- and stereoselective steroid hydroxylation by CYP109A2 from Bacillus megaterium explored by X-ray crystallography and computational modeling. Authors: Jozwik, I.K. / Bombino, E. / Abdulmughni, A. / Hartz, P. / Rozeboom, H.J. / Wijma, H.J. / Kappl, R. / Janssen, D.B. / Bernhardt, R. / Thunnissen, A.W.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8abr.cif.gz | 251 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8abr.ent.gz | 204.9 KB | Display | PDB format |
PDBx/mmJSON format | 8abr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/8abr ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abr | HTTPS FTP |
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-Related structure data
Related structure data | 8absC 5ofqS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46986.395 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Priestia megaterium DSM 319 (bacteria) / Strain: DSM 319 / Gene: BMD_2035 / Production host: Escherichia coli (E. coli) References: UniProt: D5DF88, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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-Non-polymers , 5 types, 105 molecules
#2: Chemical | ChemComp-HEB / | ||
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#3: Chemical | ChemComp-6NA / | ||
#4: Chemical | ChemComp-OCA / | ||
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.4-0.55 M ammonium sulfate, 1.05-1.2 M lithium sulfate and 0.1 M sodium citrate buffer, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→94.01 Å / Num. obs: 35461 / % possible obs: 100 % / Redundancy: 26 % / Biso Wilson estimate: 55.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.013 / Rrim(I) all: 0.066 / Net I/σ(I): 27.6 / Num. measured all: 922831 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OFQ Resolution: 2.1→41.6 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 23.95 / Stereochemistry target values: ML
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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 max: 147.3 Å2 / Biso mean: 71.9354 Å2 / Biso min: 44.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→41.6 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 14.1242 Å / Origin y: -8.9434 Å / Origin z: 17.0145 Å
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Refinement TLS group |
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