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Yorodumi- PDB-8abs: Crystal structure of CYP109A2 from Bacillus megaterium bound with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8abs | |||||||||
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Title | Crystal structure of CYP109A2 from Bacillus megaterium bound with testosterone and putative ligand 4,6-dimethyloctanoic acid | |||||||||
Components | Cytochrome P450 | |||||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / Testosterone / Fatty acid / Steroid / Complex | |||||||||
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 / molecular replacement / Resolution: 1.75 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 | 8abs.cif.gz | 254.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8abs.ent.gz | 207.6 KB | Display | PDB format |
PDBx/mmJSON format | 8abs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8abs_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8abs_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8abs_validation.xml.gz | 18 KB | Display | |
Data in CIF | 8abs_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/8abs ftp://data.pdbj.org/pub/pdb/validation_reports/ab/8abs | HTTPS FTP |
-Related structure data
Related structure data | 8abrC 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, 158 molecules
#2: Chemical | ChemComp-HEB / | ||
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#3: Chemical | ChemComp-W2L / ( | ||
#4: Chemical | ChemComp-TES / | ||
#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: 3.04 Å3/Da / Density % sol: 59.58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein was concentrated to 33 mg/ml in 50 mM citrate buffer, pH 5.5, 0.1 mM testosterone. The crystallization reservoir solution contained 0.4-0.55 M ammonium sulfate, 1.05-1.2 M lithium ...Details: Protein was concentrated to 33 mg/ml in 50 mM citrate buffer, pH 5.5, 0.1 mM testosterone. The crystallization reservoir solution contained 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: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 25, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→48.84 Å / Num. obs: 59408 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 35.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Net I/σ(I): 13.9 / Num. measured all: 335918 / Scaling rejects: 217 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OFQ Resolution: 1.75→48.84 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.12 / 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: 195.01 Å2 / Biso mean: 50.0764 Å2 / Biso min: 28.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.75→48.84 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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Refinement TLS params. | Method: refined / Origin x: 14.2027 Å / Origin y: -8.6148 Å / Origin z: 16.9267 Å
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Refinement TLS group |
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