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- PDB-5ipy: Crystal structure of WT RnTmm -

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Basic information

Entry
Database: PDB / ID: 5ipy
TitleCrystal structure of WT RnTmm
ComponentsFlavin-containing monooxygenase
KeywordsFLAVOPROTEIN / flavin-containing monooxygenase
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesRoseovarius nubinhibens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, C.Y. / Zhang, Y.Z.
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
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)106,5836
Polymers103,5252
Non-polymers3,0584
Water26,9141494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-36 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.497, 85.388, 79.533
Angle α, β, γ (deg.)90.00, 113.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flavin-containing monooxygenase


Mass: 51762.688 Da / Num. of mol.: 2 / Mutation: E153A, D154A
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 (E. coli) / References: UniProt: A3SLM3
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1494 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate (pH 6.5) and 20% (w/v) polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 142377 / % possible obs: 98.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 31
Reflection shellResolution: 1.5→1.55 Å

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
Cootmodel building
HKL-3000data scaling
HKL-3000phasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XVE

2xve


Resolution: 1.5→42.14 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 0 / Phase error: 15.39
RfactorNum. reflection% reflection
Rfree0.169 7056 5.01 %
Rwork0.146 --
obs0.147 140816 97.4 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Bsol: 41.83 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2777 Å20 Å2-0.6384 Å2
2--2.0068 Å20 Å2
3----0.7291 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 202 1494 8856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067634
X-RAY DIFFRACTIONf_angle_d1.16610407
X-RAY DIFFRACTIONf_dihedral_angle_d19.8872871
X-RAY DIFFRACTIONf_chiral_restr0.0771042
X-RAY DIFFRACTIONf_plane_restr0.0051324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4993-1.51640.2192020.16743921X-RAY DIFFRACTION87
1.5164-1.53420.20322280.15684340X-RAY DIFFRACTION95
1.5342-1.55290.18972120.15524333X-RAY DIFFRACTION95
1.5529-1.57260.20072070.15434347X-RAY DIFFRACTION95
1.5726-1.59330.17672470.14844294X-RAY DIFFRACTION94
1.5933-1.61510.1852160.14554410X-RAY DIFFRACTION97
1.6151-1.63820.18152310.14544437X-RAY DIFFRACTION97
1.6382-1.66260.18752350.13734452X-RAY DIFFRACTION97
1.6626-1.68860.17442450.13934456X-RAY DIFFRACTION97
1.6886-1.71630.16482360.13424468X-RAY DIFFRACTION98
1.7163-1.74590.1632300.13554468X-RAY DIFFRACTION98
1.7459-1.77770.17762330.13814480X-RAY DIFFRACTION98
1.7777-1.81180.17572100.14154546X-RAY DIFFRACTION98
1.8118-1.84880.18132300.13964550X-RAY DIFFRACTION98
1.8488-1.8890.17242490.14324413X-RAY DIFFRACTION98
1.889-1.9330.17282240.1484478X-RAY DIFFRACTION97
1.933-1.98130.17362330.1484398X-RAY DIFFRACTION96
1.9813-2.03490.17522470.15084452X-RAY DIFFRACTION98
2.0349-2.09480.1712580.15354531X-RAY DIFFRACTION99
2.0948-2.16240.18162650.15434519X-RAY DIFFRACTION99
2.1624-2.23970.172550.1484500X-RAY DIFFRACTION99
2.2397-2.32930.16472410.14674519X-RAY DIFFRACTION99
2.3293-2.43530.16762230.14834579X-RAY DIFFRACTION99
2.4353-2.56370.16542840.14844521X-RAY DIFFRACTION99
2.5637-2.72430.17612270.1524531X-RAY DIFFRACTION98
2.7243-2.93460.19182300.15644484X-RAY DIFFRACTION97
2.9346-3.22980.16962390.14824564X-RAY DIFFRACTION100
3.2298-3.69690.15122470.13474564X-RAY DIFFRACTION99
3.6969-4.65680.1342410.12114585X-RAY DIFFRACTION99
4.6568-42.15410.15322310.16284620X-RAY DIFFRACTION98

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