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- PDB-7olf: Crystal structure of FMNH2-dependent monooxygenase from Agrobacte... -

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Basic information

Entry
Database: PDB / ID: 7olf
TitleCrystal structure of FMNH2-dependent monooxygenase from Agrobacterium tumefaciens for oxidative desulfurization of sulfoquinovose
ComponentsMethanesulfonate sulfonatase
KeywordsOXIDOREDUCTASE / Sulfoquinovose / monooxygenase / falvin-dependent / native
Function / homologyLuciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / Methanesulfonate sulfonatase
Function and homology information
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-170 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria.
Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / ...Authors: Sharma, M. / Lingford, J.P. / Petricevic, M. / Snow, A.J.D. / Zhang, Y. / Jarva, M.A. / Mui, J.W. / Scott, N.E. / Saunders, E.C. / Mao, R. / Epa, R. / da Silva, B.M. / Pires, D.E.V. / Ascher, D.B. / McConville, M.J. / Davies, G.J. / Williams, S.J. / Goddard-Borger, E.D.
History
DepositionMay 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methanesulfonate sulfonatase
B: Methanesulfonate sulfonatase


Theoretical massNumber of molelcules
Total (without water)87,2582
Polymers87,2582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, the protein exists as dimer in solution, verified by SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-22 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.762, 203.762, 110.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 1 - 385 / Label seq-ID: 1 - 385

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

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Components

#1: Protein Methanesulfonate sulfonatase


Mass: 43628.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu3279 / Plasmid: pet29(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CEY7

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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: 3.8 Å3/Da / Density % sol: 67.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 M MES pH 6, 26% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.4→48.94 Å / Num. obs: 19137 / % possible obs: 99.9 % / Redundancy: 15.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.031 / Rrim(I) all: 0.123 / Net I/σ(I): 16 / Num. measured all: 302552 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.4-3.678.90.3643424838640.9720.1270.3875.199.9
9-48.9421.20.0522460511630.9990.0120.05347.699.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BALBES

Resolution: 3.4→48 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.895 / SU B: 25.926 / SU ML: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 1002 5.2 %RANDOM
Rwork0.2183 ---
obs0.2206 18114 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 221.83 Å2 / Biso mean: 75.274 Å2 / Biso min: 35.29 Å2
Baniso -1Baniso -2Baniso -3
1-5.06 Å22.53 Å20 Å2
2--5.06 Å20 Å2
3----16.43 Å2
Refinement stepCycle: final / Resolution: 3.4→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5392 0 0 0 5392
Num. residues----738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135517
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174884
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6417525
X-RAY DIFFRACTIONr_angle_other_deg1.2471.57211148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3155734
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45120.649262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.21915751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8851540
X-RAY DIFFRACTIONr_chiral_restr0.0610.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026447
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021289
Refine LS restraints NCS

Ens-ID: 1 / Number: 10874 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.4→3.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 79 -
Rwork0.319 1296 -
all-1375 -
obs--99.71 %

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