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- PDB-8aq8: FAD-dependent monooxygenase from Stenotrophomonas maltophilia -

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Basic information

Entry
Database: PDB / ID: 8aq8
TitleFAD-dependent monooxygenase from Stenotrophomonas maltophilia
ComponentsMonooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase / FAD-dependent / Antibiotic resistance
Function / homologyFAD-binding domain / FAD binding domain / FAD binding / monooxygenase activity / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / NITRATE ION / DI(HYDROXYETHYL)ETHER / Monooxygenase
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMaly, M. / Kolenko, P. / Duskova, J. / Skalova, T. / Dohnalek, J.
Funding supportEuropean Union, Czech Republic, 5items
OrganizationGrant numberCountry
European Regional Development FundNo. CZ.02.1.01/0.0/0.0/18_046/0015974European Union
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447European Union
Czech Academy of Sciences86652036 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000778European Union
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia.
Authors: Maly, M. / Kolenko, P. / Stransky, J. / Svecova, L. / Duskova, J. / Koval', T. / Skalova, T. / Trundova, M. / Adamkova, K. / Cerny, J. / Bozikova, P. / Dohnalek, J.
History
DepositionAug 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Monooxygenase
BBB: Monooxygenase
CCC: Monooxygenase
DDD: Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,96425
Polymers156,7174
Non-polymers4,24721
Water20,0151111
1
AAA: Monooxygenase
hetero molecules


  • defined by author
  • Evidence: SAXS, Monomer - SAXS data fit monomeric model with chi squared equal 1.05 (GNOM)., gel filtration, Monomer - estimated molar mass is 40 kDa (calibration curve of Superdex 75 Increase 10/300 GL).
  • 40.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)40,4859
Polymers39,1791
Non-polymers1,3058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Monooxygenase
hetero molecules


  • defined by author
  • 40.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)40,1245
Polymers39,1791
Non-polymers9454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Monooxygenase
hetero molecules


  • defined by author
  • 40.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)40,1866
Polymers39,1791
Non-polymers1,0075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: Monooxygenase
hetero molecules


  • defined by author
  • 40.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)40,1685
Polymers39,1791
Non-polymers9894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.932, 160.535, 95.563
Angle α, β, γ (deg.)90.000, 95.914, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 3 - 357 / Label seq-ID: 5 - 359

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AAAA
221BBBB
332AAAA
442CCCC
553AAAA
663DDDD
774BBBB
884CCCC
995BBBB
10105DDDD
11116CCCC
12126DDDD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
Monooxygenase /


Mass: 39179.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: FAD-dependent protein. The reference UniProt sequence A0A2Y9UCL1 is not the sequence of the target protein. The real sequence of the target protein is the NCBI reference sequence WP_ ...Details: FAD-dependent protein. The reference UniProt sequence A0A2Y9UCL1 is not the sequence of the target protein. The real sequence of the target protein is the NCBI reference sequence WP_049406473.1 from the complete genome of Stenotrophomonas maltophilia, strain AB550, GenBank entry CP028899.1.
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Gene: B9Y88_09170 / Plasmid: pET28a+TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lemo / References: UniProt: A0A2Y9UCL1

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Non-polymers , 7 types, 1132 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: Plate-shaped
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% (w/v) PEG 8000, 24% (v/v) ethylene glycol, 60 mM sodium nitrate, 60 mM disodium hydrogen phosphate, 60 mM ammonium sulfate, 100 mM MES/imidazole pH 6.5, 4% acetone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.95→48.26 Å / Num. obs: 98291 / % possible obs: 85.3 % / Observed criterion σ(I): -3.7 / Redundancy: 4.8 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.07 / Rrim(I) all: 0.156 / Net I/σ(I): 8.6
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4915 / CC1/2: 0.378 / Rpim(I) all: 0.729 / Rrim(I) all: 1.702 / % possible all: 48.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
MoRDaphasing
PHASERphasing
Cootmodel building
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N04

6n04


Resolution: 1.95→48.26 Å / Cor.coef. Fo:Fc: 0.95 / SU B: 5.09 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.201
RfactorNum. reflection% reflectionSelection details
Rfree0.241 5781 5 %Random selection
Rwork0.2002 98291 --
all0.202 ---
obs0.2022 98291 85.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.027 Å20 Å2-0.047 Å2
2--0.1 Å20 Å2
3----0.115 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10327 0 276 1111 11714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310966
X-RAY DIFFRACTIONr_bond_other_d0.0010.01510290
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.63714942
X-RAY DIFFRACTIONr_angle_other_deg1.3141.57723540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67451393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30820.215605
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.848151661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.71215116
X-RAY DIFFRACTIONr_chiral_restr0.0740.21420
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022639
X-RAY DIFFRACTIONr_nbd_refined0.2020.22068
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.29629
X-RAY DIFFRACTIONr_nbtor_refined0.1580.25099
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2826
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1210.212
X-RAY DIFFRACTIONr_nbd_other0.2120.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.218
X-RAY DIFFRACTIONr_mcbond_it2.7282.8325504
X-RAY DIFFRACTIONr_mcbond_other2.7292.8325503
X-RAY DIFFRACTIONr_mcangle_it4.3844.2296874
X-RAY DIFFRACTIONr_mcangle_other4.3754.2276869
X-RAY DIFFRACTIONr_scbond_it3.1893.1995462
X-RAY DIFFRACTIONr_scbond_other3.1893.1995463
X-RAY DIFFRACTIONr_scangle_it5.1364.658057
X-RAY DIFFRACTIONr_scangle_other5.1364.658058
X-RAY DIFFRACTIONr_lrange_it7.86233.61612254
X-RAY DIFFRACTIONr_lrange_other7.79933.25812019
X-RAY DIFFRACTIONr_ncsr_local_group_10.0630.0510554
X-RAY DIFFRACTIONr_ncsr_local_group_20.0560.0510620
X-RAY DIFFRACTIONr_ncsr_local_group_30.0660.0510514
X-RAY DIFFRACTIONr_ncsr_local_group_40.0590.0510545
X-RAY DIFFRACTIONr_ncsr_local_group_50.0570.0510476
X-RAY DIFFRACTIONr_ncsr_local_group_60.0640.0510467
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.062570.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.062570.05009
23AAAX-RAY DIFFRACTIONLocal ncs0.056180.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.056180.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.065540.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.065540.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.059250.05008
48CCCX-RAY DIFFRACTIONLocal ncs0.059250.05008
59BBBX-RAY DIFFRACTIONLocal ncs0.056970.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.056970.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.064140.05008
612DDDX-RAY DIFFRACTIONLocal ncs0.064140.05008
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.366 195 -
Rwork0.336 --
all0.337 3966 -
obs-3771 46.72 %

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