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- PDB-4uwm: Type II Baeyer-Villiger monooxygenase.The oxygenating constituent... -

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Basic information

Entry
Database: PDB / ID: 4uwm
TitleType II Baeyer-Villiger monooxygenase.The oxygenating constituent of 3,6-diketocamphane monooxygenase from CAM plasmid of Pseudomonas putida in complex with FMN.
Components3,6-DIKETOCAMPHANE 1,6 MONOOXYGENASE
KeywordsOXIDOREDUCTASE / BIOCATALYSIS
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 / cytosol
Similarity search - Function
: / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 3,6-diketocamphane 1,6-monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIsupov, 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: 1998
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Oxygenating Subunit of 3,6- Diketocamphane Monooxygenase from Pseudomonas Putida.
Authors: Mcghie, E.J. / Isupov, M.N. / Schroder, E. / Littlechild, J.A.
History
DepositionAug 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,6-DIKETOCAMPHANE 1,6 MONOOXYGENASE
B: 3,6-DIKETOCAMPHANE 1,6 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,79612
Polymers84,7262
Non-polymers2,07010
Water11,097616
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-16.1 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.790, 82.840, 149.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99819, 0.06005, -0.00383), (0.06015, 0.99437, -0.08719), (-0.00142, -0.08726, -0.99618)
Vector: -35.02756, 4.33083, 73.92238)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3,6-DIKETOCAMPHANE 1,6 MONOOXYGENASE / 3 / 6-DKCMO / 3 / 6-DIKETOCAMPHANE 1 / 6-MONOOXYGENASE OXYGENATING SUBUNIT / BAEYER-VILLIGER ...3 / 6-DKCMO / 3 / 6-DIKETOCAMPHANE 1 / 6-MONOOXYGENASE OXYGENATING SUBUNIT / BAEYER-VILLIGER MONOOXYGENASE / BVMO / CAMPHOR 1 / 6-MONOOXY GENASE / TYPE II BAEYER-VILLIGER MONOOXYGENASE


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, 626 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7 / Details: 100 MM HEPES PH 7.0 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→55.57 Å / Num. obs: 71800 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WGK

2wgk
PDB Unreleased entry


Resolution: 1.9→74.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.599 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.138
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 3638 5.1 %RANDOM
Rwork0.18344 ---
obs0.18536 68090 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.086 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→74.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5745 0 139 616 6500
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196671
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9699142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98123.723325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.186151167
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9061547
X-RAY DIFFRACTIONr_chiral_restr0.0890.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215199
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6656.1893074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.24311.5353878
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1526.8883597
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 264 -
Rwork0.283 4882 -
obs--97.72 %

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