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- PDB-6uug: Structure of methanesulfinate monooxygenase MsuC from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 6uug
TitleStructure of methanesulfinate monooxygenase MsuC from Pseudomonas fluorescens at 1.69 angstrom resolution
ComponentsPutative dehydrogenase
KeywordsFLAVOPROTEIN / two-component flavin-dependent monooxygenase / methyl sulfur assimilation / dimethylsulfide / global sulfur cycle
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors / monooxygenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily ...Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, C-terminal domain / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Putative dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.685 Å
AuthorsSoule, J. / Gnann, A.D. / Gonzalez, R. / Parker, M.J. / McKenna, K.C. / Nguyen, S.V. / Phan, N.T. / Wicht, D.K. / Dowling, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1807480 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structure and function of the two-component flavin-dependent methanesulfinate monooxygenase within bacterial sulfur assimilation.
Authors: Soule, J. / Gnann, A.D. / Gonzalez, R. / Parker, M.J. / McKenna, K.C. / Nguyen, S.V. / Phan, N.T. / Wicht, D.K. / Dowling, D.P.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3May 6, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 11, 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: Putative dehydrogenase
B: Putative dehydrogenase


Theoretical massNumber of molelcules
Total (without water)92,5162
Polymers92,5162
Non-polymers00
Water6,684371
1
A: Putative dehydrogenase
B: Putative dehydrogenase

A: Putative dehydrogenase
B: Putative dehydrogenase


Theoretical massNumber of molelcules
Total (without water)185,0324
Polymers185,0324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13600 Å2
ΔGint-95 kcal/mol
Surface area53320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.187, 161.582, 62.045
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Putative dehydrogenase /


Mass: 46258.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain Pf0-1) (bacteria)
Strain: Pf0-1 / Gene: Pfl01_3917 / Plasmid: pPfl01_msuC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K9A0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.28 Å3/Da / Density % sol: 45.95 % / Description: trapezoidal shaped, small crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris (pH 8.5) 0.15 M CaCl2 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.68→62.045 Å / Num. obs: 92686 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.2 Å2 / CC1/2: 1 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Rsym value: 0.041 / Net I/σ(I): 20.32
Reflection shellResolution: 1.68→1.79 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.42 / Num. unique obs: 14648 / CC1/2: 0.655 / Rpim(I) all: 0.479 / Rsym value: 1.164 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSVERSION Mar 15, 2019data reduction
XDSVERSION Mar 15, 2019data scaling
PHASER2.5.6phasing
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XB8

5xb8


Resolution: 1.685→62.045 Å / Cross valid method: FREE R-VALUE
Details: Rounds of simulated annealing, minimization, and B-factor refinement were conducted until convergence. Occupancies of alternate side-chain conformations were optimized towards the end of refinement.
RfactorNum. reflection% reflection
Rfree0.2082 4633 5 %
Rwork0.1852 --
obs0.1864 87979 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.85 Å2
Refinement stepCycle: LAST / Resolution: 1.685→62.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6038 0 0 371 6409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00626272
X-RAY DIFFRACTIONf_angle_d0.76348543
X-RAY DIFFRACTIONf_chiral_restr0.0496937
X-RAY DIFFRACTIONf_plane_restr0.00491114
X-RAY DIFFRACTIONf_dihedral_angle_d15.99873724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.750.31524990.28869471X-RAY DIFFRACTION98.09
1.75-1.830.26915110.23789706X-RAY DIFFRACTION99.88
1.83-1.930.26645120.22289710X-RAY DIFFRACTION99.94
1.93-2.050.25255090.20389674X-RAY DIFFRACTION99.92
2.05-2.210.21035130.18269732X-RAY DIFFRACTION99.78
2.21-2.430.23015080.18989757X-RAY DIFFRACTION99.92
2.43-2.780.22045200.19079819X-RAY DIFFRACTION99.91
2.78-3.510.21155210.18739876X-RAY DIFFRACTION99.94
3.51-62.090.1825400.170510234X-RAY DIFFRACTION99.83

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