+Open data
-Basic information
Entry | Database: PDB / ID: 4ap1 | ||||||
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Title | Oxidized steroid monooxygenase bound to NADP | ||||||
Components | STEROID MONOOXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / BAEYER-VILLIGER / FLAVIN | ||||||
Function / homology | Function and homology information N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | RHODOCOCCUS RHODOCHROUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Franceschini, S. / van Beek, H.L. / Martinoli, C. / Pennetta, A. / Fraaije, M.W. / Mattevi, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Exploring the Structural Basis of Substrate Preferences in Baeyer-Villiger Monooxygenases: Insight from Steroid Monooxygenase. Authors: Franceschini, S. / Van Beek, H.L. / Pennetta, A. / Martinoli, C. / Fraaije, M.W. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ap1.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ap1.ent.gz | 174.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ap1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ap1_validation.pdf.gz | 942.2 KB | Display | wwPDB validaton report |
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Full document | 4ap1_full_validation.pdf.gz | 954.3 KB | Display | |
Data in XML | 4ap1_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 4ap1_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/4ap1 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/4ap1 | HTTPS FTP |
-Related structure data
Related structure data | 4aosSC 4aoxC 4ap3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 60142.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOCOCCUS RHODOCHROUS (bacteria) / Plasmid: PET-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O50641, EC: 1.14.13.54 |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.2 % / Description: NONE |
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Crystal grow | pH: 6.2 / Details: 1.9M MGSO4, 0.1M MES PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→58.1 Å / Num. obs: 17327 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.95→3.11 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AOS Resolution: 2.95→58.1 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.911 / SU B: 21.068 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-19 AND 511-517 ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.596 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→58.1 Å
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Refine LS restraints |
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