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- PDB-5gsn: Tmm in complex with methimazole -

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Basic information

Entry
Database: PDB / ID: 5gsn
TitleTmm in complex with methimazole
ComponentsFlavin-containing monooxygenase
KeywordsFLAVOPROTEIN / flavin-containing monoxygenase / complex
Function / homology
Function and homology information


trimethylamine monooxygenase / N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / 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 / 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesRoseovarius nubinhibens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsZhang, Y.Z. / Li, C.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation of China31290230 China
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Structural mechanism for bacterial oxidation of oceanic trimethylamine into trimethylamine N-oxide
Authors: Li, C.Y. / Chen, X.L. / Zhang, D. / Wang, P. / Sheng, Q. / Peng, M. / Xie, B.B. / Qin, Q.L. / Li, P.Y. / Zhang, X.Y. / Su, H.N. / Song, X.Y. / Shi, M. / Zhou, B.C. / Xun, L.Y. / Chen, Y. / Zhang, Y.Z.
History
DepositionAug 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flavin-containing monooxygenase
B: Flavin-containing monooxygenase
C: Flavin-containing monooxygenase
D: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,09114
Polymers206,7464
Non-polymers6,34410
Water14,160786
1
A: Flavin-containing monooxygenase
hetero molecules

C: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6598
Polymers103,3732
Non-polymers3,2866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area9760 Å2
ΔGint-32 kcal/mol
Surface area31560 Å2
MethodPISA
2
B: Flavin-containing monooxygenase
hetero molecules

D: Flavin-containing monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4316
Polymers103,3732
Non-polymers3,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area8810 Å2
ΔGint-40 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.849, 207.578, 72.517
Angle α, β, γ (deg.)90.00, 90.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Flavin-containing monooxygenase


Mass: 51686.594 Da / Num. of mol.: 4 / Mutation: E153A, D154A, Y207S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM) (bacteria)
Strain: ATCC BAA-591 / DSM 15170 / ISM / Gene: ISM_08155 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A3SLM3
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-MMZ / 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE / METHIMAZOLE


Mass: 114.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2S / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 786 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate, 0.1 M Bis-Tris propane (pH 6.5) and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 84044 / % possible obs: 93.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.7 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-3000data scaling
HKL-3000data processing
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IPY

5ipy


Resolution: 2.203→46.737 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 4066 5.04 %
Rwork0.203 --
obs0.2066 80597 89.09 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.298 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6015 Å20 Å2-2.4799 Å2
2--9.3276 Å20 Å2
3----6.7261 Å2
Refinement stepCycle: LAST / Resolution: 2.203→46.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14292 0 418 786 15496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815240
X-RAY DIFFRACTIONf_angle_d1.16320774
X-RAY DIFFRACTIONf_dihedral_angle_d20.5655790
X-RAY DIFFRACTIONf_chiral_restr0.0752098
X-RAY DIFFRACTIONf_plane_restr0.0042642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2026-2.22850.34051230.24572106X-RAY DIFFRACTION72
2.2285-2.25570.36411090.2422492X-RAY DIFFRACTION82
2.2557-2.28430.34031500.25952491X-RAY DIFFRACTION86
2.2843-2.31430.37691350.22622497X-RAY DIFFRACTION85
2.3143-2.3460.31891140.21122530X-RAY DIFFRACTION84
2.346-2.37950.31221320.20042539X-RAY DIFFRACTION87
2.3795-2.41510.34711280.23482560X-RAY DIFFRACTION86
2.4151-2.45280.33591360.23962546X-RAY DIFFRACTION87
2.4528-2.4930.35971240.26222611X-RAY DIFFRACTION87
2.493-2.5360.38531470.26992587X-RAY DIFFRACTION87
2.536-2.58210.32661500.24682555X-RAY DIFFRACTION88
2.5821-2.63180.32951360.24192595X-RAY DIFFRACTION88
2.6318-2.68550.30391420.22512628X-RAY DIFFRACTION89
2.6855-2.74390.34241320.22942628X-RAY DIFFRACTION90
2.7439-2.80770.31191250.22062641X-RAY DIFFRACTION88
2.8077-2.87790.28931440.22612663X-RAY DIFFRACTION90
2.8779-2.95570.3411530.23032610X-RAY DIFFRACTION89
2.9557-3.04260.26361370.21522668X-RAY DIFFRACTION89
3.0426-3.14080.30991260.22012667X-RAY DIFFRACTION90
3.1408-3.25310.31761510.22492691X-RAY DIFFRACTION92
3.2531-3.38330.2511520.21592758X-RAY DIFFRACTION92
3.3833-3.53720.28841450.20962699X-RAY DIFFRACTION93
3.5372-3.72360.26591370.18992784X-RAY DIFFRACTION94
3.7236-3.95680.26251590.17152757X-RAY DIFFRACTION93
3.9568-4.26210.21541470.15912765X-RAY DIFFRACTION93
4.2621-4.69070.17551610.14072832X-RAY DIFFRACTION96
4.6907-5.36860.19791570.15882851X-RAY DIFFRACTION97
5.3686-6.76060.25111680.19722894X-RAY DIFFRACTION96
6.7606-46.74750.21731460.19022886X-RAY DIFFRACTION96

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