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- PDB-5aec: Type II Baeyer-Villiger monooxygenase.The oxygenating constituent... -

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Basic information

Entry
Database: PDB / ID: 5aec
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 / 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
Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3,6-diketocamphane 1,6-monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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: 2008
Title: Ncs-Constrained Exhaustive Search Using Oligomeric Models.
Authors: Isupov, M.N. / Lebedev, A.A.
History
DepositionAug 28, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionSep 9, 2015ID: 2WGK
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 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)86,87023
Polymers84,7262
Non-polymers2,14421
Water14,376798
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-137.2 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.963, 93.317, 161.893
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: (0.10255, 0.94555, 0.3089), (0.94711, -0.18774, 0.26026), (0.30408, 0.26588, -0.91479)
Vector: -38.55143, 19.5296, 79.14034)

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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 / CAMPHOR 1 / 6-MONOOXYGENASE / BVMO / 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, 819 molecules

#2: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID / PIPES


Mass: 302.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5
Details: 50 MM PIPES PH 6.5, 50 % SATURATION AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8443
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8443 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.93→1.98 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 88.3

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Processing

Software
NameVersionClassification
CCP4model building
Aimlessdata scaling
MOLREPphasing
MLPHAREphasing
DMphasing
CCP4phasing
REFMAC5.8.0131refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LUC

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
RfactorNum. reflection% reflectionSelection details
Rfree0.22139 3097 5 %RANDOM
Rwork0.17138 ---
obs0.17388 59253 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.93→80.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 126 798 6703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196617
X-RAY DIFFRACTIONr_bond_other_d0.0050.026309
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9679059
X-RAY DIFFRACTIONr_angle_other_deg1.177314662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75723.589326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.807151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0351550
X-RAY DIFFRACTIONr_chiral_restr0.0840.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217493
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021565
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_it4.2356.1943070
X-RAY DIFFRACTIONr_mcbond_other4.2386.1883069
X-RAY DIFFRACTIONr_mcangle_it5.78310.3333867
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5597.4323547
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: 1.933→1.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 196 -
Rwork0.281 3878 -
obs--88.84 %

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