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- PDB-7d4k: Crystal structure of Tmm from Pelagibacter sp. strain HTCC7211 -

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Basic information

Entry
Database: PDB / ID: 7d4k
TitleCrystal structure of Tmm from Pelagibacter sp. strain HTCC7211
ComponentsFlavin-containing monooxygenase FMO
KeywordsFLAVOPROTEIN / trimethylamine 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 superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Trimethylamine monooxygenase
Similarity search - Component
Biological speciesCandidatus Pelagibacter sp. HTCC7211 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLi, C.Y. / Zhang, Y.Z.
CitationJournal: Front Microbiol / Year: 2021
Title: Structural and Mechanistic Insights Into Dimethylsulfoxide Formation Through Dimethylsulfide Oxidation.
Authors: Wang, X.J. / Zhang, N. / Teng, Z.J. / Wang, P. / Zhang, W.P. / Chen, X.L. / Zhang, Y.Z. / Chen, Y. / Fu, H.H. / Li, C.Y.
History
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: 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
A: Flavin-containing monooxygenase FMO
B: Flavin-containing monooxygenase FMO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3166
Polymers108,2582
Non-polymers3,0584
Water15,313850
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-39 kcal/mol
Surface area31940 Å2
Unit cell
Length a, b, c (Å)69.415, 82.076, 97.907
Angle α, β, γ (deg.)90.000, 98.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flavin-containing monooxygenase FMO / Trimethylamine monooxygenase


Mass: 54129.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Pelagibacter sp. HTCC7211 (bacteria)
Gene: PB7211_242 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6BQB2
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium citrate tribasic, 0.1 M imidazole (pH 7.0) and 20% (w/v) polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. obs: 98662 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.35 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.068 / Rrim(I) all: 0.126 / Χ2: 2.433 / Net I/σ(I): 5.9 / Num. measured all: 325628
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.492 / Num. unique obs: 4991 / CC1/2: 0.969 / Rpim(I) all: 0.058 / Rrim(I) all: 0.107 / Χ2: 11.663 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data collection
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IPY

5ipy


Resolution: 1.8→48.55 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 4680 5.01 %
Rwork0.217 88657 -
obs0.219 93337 92.1 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.58 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 90.11 Å2 / Biso mean: 30.61 Å2 / Biso min: 16.72 Å2
Baniso -1Baniso -2Baniso -3
1-12.957 Å20 Å2-1.8114 Å2
2---4.6326 Å20 Å2
3----8.3244 Å2
Refinement stepCycle: final / Resolution: 1.8→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 202 850 8338
Biso mean--24.04 38.38 -
Num. residues----884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067774
X-RAY DIFFRACTIONf_angle_d1.13510549
X-RAY DIFFRACTIONf_chiral_restr0.0751061
X-RAY DIFFRACTIONf_plane_restr0.0051332
X-RAY DIFFRACTIONf_dihedral_angle_d17.7583067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.81690.33291130.2885195561
1.8169-1.83830.34381440.2639268984
1.8383-1.86070.29211390.241270185
1.8607-1.88420.28161260.2327278486
1.8842-1.9090.30531400.23273286
1.909-1.93520.30141380.226287489
1.9352-1.96280.2741360.228285589
1.9628-1.99210.27411570.2333285890
1.9921-2.02330.27261620.2243289992
2.0233-2.05640.28031540.2233293492
2.0564-2.09190.27971570.214291991
2.0919-2.12990.25881400.2132301794
2.1299-2.17090.24771580.2148304995
2.1709-2.21520.24741600.2163297995
2.2152-2.26340.2541590.2181304295
2.2634-2.3160.27771640.2082305695
2.316-2.37390.24051560.2092306596
2.3739-2.43810.25581830.2083305896
2.4381-2.50990.24651640.2092304195
2.5099-2.59090.24961760.2153306496
2.5909-2.68350.25851560.2115314497
2.6835-2.79090.22891790.2068311898
2.7909-2.91790.24341700.2163313298
2.9179-3.07170.28081640.2288314198
3.0717-3.26410.23451610.2218309996
3.2641-3.51610.25391670.2171311697
3.5161-3.86980.2381740.2093311596
3.8698-4.42940.19981680.1904302294
4.4294-5.57930.22081580.2051301092
5.5793-48.550.2811570.2511318996
Refinement TLS params.Method: refined / Origin x: -25.0931 Å / Origin y: 0.2716 Å / Origin z: -23.1399 Å
111213212223313233
T0.1956 Å20 Å2-0.0011 Å2-0.2041 Å20.0069 Å2--0.2014 Å2
L0.123 °20.0024 °2-0.0196 °2-0.2732 °20.1476 °2--0.2791 °2
S-0.0062 Å °0.003 Å °0.0015 Å °-0 Å °-0.0054 Å °-0.022 Å °0.0141 Å °0.0096 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 444
2X-RAY DIFFRACTION1ALLA501 - 1044
3X-RAY DIFFRACTION1ALLB2 - 441
4X-RAY DIFFRACTION1ALLB501 - 1006

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