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- PDB-4a9w: Flavin-containing monooxygenase from Stenotrophomonas maltophilia -

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Basic information

Entry
Database: PDB / ID: 4a9w
TitleFlavin-containing monooxygenase from Stenotrophomonas maltophilia
ComponentsMONOOXYGENASE
KeywordsOXIDOREDUCTASE / BAEYER-VILLIGER / FAD
Function / homology
Function and homology information


monooxygenase activity / flavin adenine dinucleotide binding
Similarity search - Function
: / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Monooxygenase
Similarity search - Component
Biological speciesSTENOTROPHOMONAS MALTOPHILIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsJensen, C.N. / Cartwright, J. / Hart, S. / Turkenburg, J.P. / Ali, S.T. / Allen, M.J. / Grogan, G.
CitationJournal: Chembiochem / Year: 2012
Title: A Flavoprotein Monooxygenase that Catalyses a Baeyer-Villiger Reaction and Thioether Oxidation Using Nadh as the Nicotinamide Cofactor.
Authors: Jensen, C.N. / Cartwright, J. / Ward, J. / Hart, S. / Turkenburg, J.P. / Ali, S.T. / Allen, M.J. / Grogan, G.
History
DepositionNov 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Other / Refinement description
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: MONOOXYGENASE
B: MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,68324
Polymers77,1912
Non-polymers3,49222
Water1,71195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-334.6 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.002, 84.002, 103.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 4 / Auth seq-ID: 1 - 352 / Label seq-ID: 1 - 352

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.380157, -0.924875, 0.009317), (-0.924915, 0.380174, -2.6E-5), (-0.003518, -0.008627, -0.999957)-0.1301, 0.08499, 36.4338

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Components

#1: Protein MONOOXYGENASE / FLAVOPROTEIN MONOOXYGENASE


Mass: 38595.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STENOTROPHOMONAS MALTOPHILIA (bacteria)
Strain: PML168 / Description: ISOLATED BY PLYMOUTH MARINE LABORATORY / Plasmid: YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2FRL2, EC: 1.14.13.8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: PROTEIN CONCENTRATION OF 4 MG ML-1. THE BEST CRYSTALS WERE ROUTINELY OBTAINED IN HANGING DROPS CONTAINING 0.9 M LITHIUM SULPHATE IN 100 MM BIS-TRIS PROPANE BUFFER AT PH 5.6.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.72→72.75 Å / Num. obs: 20682 / % possible obs: 1 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.5
Reflection shellResolution: 2.72→2.79 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CTY

3cty


Resolution: 2.72→72.75 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 12.537 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 212-233 ARE MISSING IN EACH SUBUNIT
RfactorNum. reflection% reflectionSelection details
Rfree0.23802 1115 5.1 %RANDOM
Rwork0.18194 ---
obs0.18498 20682 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.72→72.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 206 95 5300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9837338
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96422.075212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49615719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.381546
X-RAY DIFFRACTIONr_chiral_restr0.1220.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214089
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2493 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.290.5
2Bmedium positional0.290.5
1Amedium thermal3.822
2Bmedium thermal3.822
LS refinement shellResolution: 2.724→2.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 68 -
Rwork0.277 1548 -
obs--100 %

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