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- PDB-7d4m: Crystal structure of Tmm from strain HTCC7211 soaked with DMS for... -

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Basic information

Entry
Database: PDB / ID: 7d4m
TitleCrystal structure of Tmm from strain HTCC7211 soaked with DMS for 5 min
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: 1.786 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
Water19,0241056
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-39 kcal/mol
Surface area32050 Å2
Unit cell
Length a, b, c (Å)69.025, 81.837, 97.929
Angle α, β, γ (deg.)90.000, 98.120, 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.: 1056 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
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: Jan 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.786→50 Å / Num. obs: 98586 / % possible obs: 97.7 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Χ2: 2.503 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.866.90.3198950.9820.1270.3361.29798.6
1.86-1.946.80.23698690.9870.0970.2551.49998.6
1.94-2.036.70.18899360.990.0780.2041.75198.6
2.03-2.136.30.1498110.9920.060.1532.10497.7
2.13-2.276.60.11697350.9940.0490.1262.42996.8
2.27-2.446.60.09399630.9960.0390.1012.7899
2.44-2.696.30.07799880.9960.0330.0843.05799
2.69-3.085.90.06297920.9970.0280.0683.37796.9
3.08-3.886.10.05298450.9980.0220.0563.73397.2
3.88-505.90.04697520.9970.020.053.49594.9

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Processing

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

5ipy


Resolution: 1.786→44.171 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1824 4733 4.87 %
Rwork0.1625 92540 -
obs0.1636 97273 95.1 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.413 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 79.86 Å2 / Biso mean: 24.43 Å2 / Biso min: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-11.9389 Å20 Å2-0.6543 Å2
2---4.7821 Å2-0 Å2
3----7.1568 Å2
Refinement stepCycle: final / Resolution: 1.786→44.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7302 0 202 1056 8560
Biso mean--20.06 33.48 -
Num. residues----886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067772
X-RAY DIFFRACTIONf_angle_d1.15810547
X-RAY DIFFRACTIONf_chiral_restr0.0781063
X-RAY DIFFRACTIONf_plane_restr0.0051330
X-RAY DIFFRACTIONf_dihedral_angle_d17.1653069
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7861-1.80640.2305790.2016173154
1.8064-1.82760.2231410.1861305794
1.8276-1.84990.22971710.174308794
1.8499-1.87330.20671410.17303595
1.8733-1.8980.19121480.1621308896
1.898-1.9240.20991590.1612309096
1.924-1.95150.22151560.1576312196
1.9515-1.98060.18811560.1652312997
1.9806-2.01160.19271380.1592313797
2.0116-2.04450.19631640.1603316197
2.0445-2.07980.20591540.1628312197
2.0798-2.11760.21241860.1676306196
2.1176-2.15830.18921440.1663295690
2.1583-2.20240.20741530.1587317098
2.2024-2.25030.18771800.1654314398
2.2503-2.30260.18891700.1697319399
2.3026-2.36020.20611570.1626320698
2.3602-2.4240.18691900.1632314798
2.424-2.49530.19451540.1702321099
2.4953-2.57590.20641610.1712318499
2.5759-2.66790.21261600.1666320599
2.6679-2.77470.19651630.165323199
2.7747-2.9010.19941560.1717321299
2.901-3.05390.18031610.1717301594
3.0539-3.24520.16561640.1689310795
3.2452-3.49560.18091420.1638322699
3.4956-3.84720.16831850.1546315897
3.8472-4.40350.14551610.1393310896
4.4035-5.54620.13381590.1417312695
5.5462-44.1710.18591800.1805312594

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