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- PDB-5iq4: Crystal structure of RnTmm mutant Y207S soaking -

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Basic information

Entry
Database: PDB / ID: 5iq4
TitleCrystal structure of RnTmm mutant Y207S soaking
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
AuthorsZhang, Y.Z. / Li, C.Y.
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)106,6356
Polymers103,5772
Non-polymers3,0584
Water17,601977
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-36 kcal/mol
Surface area31840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.969, 61.364, 104.706
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flavin-containing monooxygenase


Mass: 51788.637 Da / Num. of mol.: 2
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.: 977 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
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. The Y207S soaking crystals were obtained using crystals of Y207S soaked with 15 mM TMA for 15 min.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 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: 130501 / % possible obs: 88.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 36.8
Reflection shellResolution: 1.5→1.53 Å

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Processing

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

5ipy


Resolution: 1.5→35.72 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 0 / Phase error: 18.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 6375 5.01 %
Rwork0.156 --
obs0.159 127197 85.8 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.91 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.517 Å20 Å21.9532 Å2
2--0.7662 Å20 Å2
3----1.2833 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7146 0 202 977 8325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057611
X-RAY DIFFRACTIONf_angle_d1.08110375
X-RAY DIFFRACTIONf_dihedral_angle_d20.0212889
X-RAY DIFFRACTIONf_chiral_restr0.0741047
X-RAY DIFFRACTIONf_plane_restr0.0041320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4985-1.51560.2892150.21954008X-RAY DIFFRACTION86
1.5156-1.53340.25812240.19924317X-RAY DIFFRACTION92
1.5334-1.55210.25942190.18894345X-RAY DIFFRACTION93
1.5521-1.57170.26542310.17734355X-RAY DIFFRACTION94
1.5717-1.59240.25882130.17464489X-RAY DIFFRACTION95
1.5924-1.61420.21432220.15694454X-RAY DIFFRACTION95
1.6142-1.63730.23882320.15174387X-RAY DIFFRACTION95
1.6373-1.66170.20532300.14014554X-RAY DIFFRACTION96
1.6617-1.68770.20292030.14124467X-RAY DIFFRACTION96
1.6877-1.71540.20772660.14364518X-RAY DIFFRACTION97
1.7154-1.74490.21532430.13584548X-RAY DIFFRACTION97
1.7449-1.77670.1972300.134534X-RAY DIFFRACTION98
1.7767-1.81080.20162440.13024587X-RAY DIFFRACTION98
1.8108-1.84780.18642620.1244487X-RAY DIFFRACTION97
1.8478-1.8880.21361610.12363447X-RAY DIFFRACTION79
1.888-1.93190.4369710.32761249X-RAY DIFFRACTION48
1.9319-1.98020.22311630.17233227X-RAY DIFFRACTION69
1.9802-2.03370.21332430.15744605X-RAY DIFFRACTION99
2.0337-2.09360.20912740.16514623X-RAY DIFFRACTION99
2.0936-2.16110.21992330.15974657X-RAY DIFFRACTION99
2.1611-2.23840.19981240.15462380X-RAY DIFFRACTION74
2.2384-2.3280.1985710.15941447X-RAY DIFFRACTION71
2.328-2.43390.21292640.15464669X-RAY DIFFRACTION100
2.4339-2.56220.20452650.15964660X-RAY DIFFRACTION100
2.5622-2.72270.19562320.15624710X-RAY DIFFRACTION100
2.7227-2.93280.20422750.16234705X-RAY DIFFRACTION100
2.9328-3.22780.19322690.16084675X-RAY DIFFRACTION100
3.2278-3.69440.19291300.15922360X-RAY DIFFRACTION76
3.6944-4.6530.14021240.12552670X-RAY DIFFRACTION61
4.653-35.72720.18142420.15244688X-RAY DIFFRACTION96

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