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Yorodumi- PDB-5aec: Type II Baeyer-Villiger monooxygenase.The oxygenating constituent... -
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-Basic information
Entry | Database: PDB / ID: 5aec | |||||||||
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Title | Type II Baeyer-Villiger monooxygenase.The oxygenating constituent of 3,6-diketocamphane monooxygenase from CAM plasmid of Pseudomonas putida in complex with FMN. | |||||||||
Components | 3,6-DIKETOCAMPHANE 1,6 MONOOXYGENASE | |||||||||
Keywords | OXIDOREDUCTASE / BIOCATALYSIS / FLAVIN MONOOXYGENASE | |||||||||
Function / homology | Function and homology information 3,6-diketocamphane 1,2-monooxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS PUTIDA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | |||||||||
Authors | Isupov, M.N. / Schroeder, E. / Gibson, R.P. / Beecher, J. / Donadio, G. / Saneei, V. / Dcunha, S. / McGhie, E.J. / Sayer, C. / Davenport, C.F. ...Isupov, M.N. / Schroeder, E. / Gibson, R.P. / Beecher, J. / Donadio, G. / Saneei, V. / Dcunha, S. / McGhie, E.J. / Sayer, C. / Davenport, C.F. / Lau, P.C. / Hasegawa, Y. / Iwaki, H. / Kadow, M. / Loschinski, K. / Bornscheuer, U.T. / Bourenkov, G. / Littlechild, J.A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: The Oxygenating Constituent of 3,6-Diketocamphane Monooxygenase from the Cam Plasmid of Pseudomonas Putida: The First Crystal Structure of a Type II Baeyer-Villiger Monooxygenase. Authors: Isupov, M.N. / Schroder, E. / Gibson, R.P. / Beecher, J. / Donadio, G. / Saneei, V. / Dcunha, S.A. / Mcghie, E.J. / Sayer, C. / Davenport, C.F. / Lau, P.C. / Hasegawa, Y. / Iwaki, H. / ...Authors: Isupov, M.N. / Schroder, E. / Gibson, R.P. / Beecher, J. / Donadio, G. / Saneei, V. / Dcunha, S.A. / Mcghie, E.J. / Sayer, C. / Davenport, C.F. / Lau, P.C. / Hasegawa, Y. / Iwaki, H. / Kadow, M. / Balke, K. / Bornscheuer, U.T. / Bourenkov, G. / Littlechild, J.A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Ncs-Constrained Exhaustive Search Using Oligomeric Models. Authors: Isupov, M.N. / Lebedev, A.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aec.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aec.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 5aec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aec_validation.pdf.gz | 896.1 KB | Display | wwPDB validaton report |
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Full document | 5aec_full_validation.pdf.gz | 899.5 KB | Display | |
Data in XML | 5aec_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 5aec_validation.cif.gz | 59.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5aec ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5aec | HTTPS FTP |
-Related structure data
Related structure data | 4uwmC 1lucS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.10255, 0.94555, 0.3089), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42362.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE OXYGENATING CONSTITUENT OF 3,6-DIKETOCAMPHANE MONOOXYGENASE FROM CAM PLASMID OF PSEUDOMONAS PUTIDA Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: NCIMB 10007 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D7UER1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor |
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-Non-polymers , 5 types, 819 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 50 MM PIPES PH 6.5, 50 % SATURATION AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8443 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8443 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→20.44 Å / Num. obs: 62419 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LUC Resolution: 1.93→80.95 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.641 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 26.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→80.95 Å
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