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- PDB-7jw9: Ternary cocrystal structure of alkanesulfonate monooxygenase MsuD... -

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Basic information

Entry
Database: PDB / ID: 7jw9
TitleTernary cocrystal structure of alkanesulfonate monooxygenase MsuD from Pseudomonas fluorescens
ComponentsAlkanesulfonate monooxygenase
KeywordsFLAVOPROTEIN / OXIDOREDUCTASE / TIM barrel
Function / homology
Function and homology information


alkanesulfonate monooxygenase / alkanesulfonate monooxygenase activity / alkanesulfonate catabolic process / nucleotide binding
Similarity search - Function
Alkanesulphonate monooxygenase, FMN-dependent / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
methanesulfonic acid / FLAVIN MONONUCLEOTIDE / Alkanesulfonate monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsLiew, J.J.M. / Dowling, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1807480 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structures of the alkanesulfonate monooxygenase MsuD provide insight into C-S bond cleavage, substrate scope, and an unexpected role for the tetramer.
Authors: Liew, J.J.M. / El Saudi, I.M. / Nguyen, S.V. / Wicht, D.K. / Dowling, D.P.
History
DepositionAug 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 7, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Oct 18, 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: Alkanesulfonate monooxygenase
B: Alkanesulfonate monooxygenase
C: Alkanesulfonate monooxygenase
D: Alkanesulfonate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,34813
Polymers177,1164
Non-polymers2,2339
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23340 Å2
ΔGint-121 kcal/mol
Surface area45980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.470, 92.470, 320.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein
Alkanesulfonate monooxygenase / FMNH2-dependent aliphatic sulfonate monooxygenase / flavin-dependent methanesulfonate monooxygenase


Mass: 44278.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: msuD, ssuD, Pfl01_3916 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K9A1, alkanesulfonate monooxygenase
#2: Chemical
ChemComp-03S / methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.24 Å3/Da / Density % sol: 45 % / Description: hexagonal
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350, sodium succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.39→46.24 Å / Num. obs: 60776 / % possible obs: 99.6 % / Redundancy: 12.835 % / Biso Wilson estimate: 50.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.035 / Rrim(I) all: 0.125 / Χ2: 1.081 / Net I/σ(I): 16.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.39-2.4512.5071.3571.9142650.7640.3981.41594.5
2.45-2.5211.5421.192.1344030.771.246100
2.52-2.5913.2551.0212.7242370.8651.062100
2.59-2.6713.0690.9053.341810.880.942100
2.67-2.7613.7730.6854.4440210.9410.712100
2.76-2.8613.5920.5275.7338720.9620.547100
2.86-2.9713.2690.4197.1437730.9720.436100
2.97-3.0912.890.3149.3936500.9830.327100
3.09-3.2213.1320.24611.9234040.9890.257100
3.22-3.3812.6830.19814.0533140.9920.20699.9
3.38-3.5711.3280.13818.5331830.9950.145100
3.57-3.7811.5640.09724.9629410.9970.102100
3.78-4.0413.4780.08230.6228140.9980.085100
4.04-4.3713.2260.06636.626290.9990.069100
4.37-4.7813.6220.05841.7623720.9990.0699.9
4.78-5.3513.1870.05939.721910.9990.061100
5.35-6.1812.7470.06136.519450.9990.063100
6.18-7.5611.3150.05238.8516000.9990.05499.9
7.56-10.713.7510.03354.86127210.034100
10.7-46.2412.5150.02853.9370910.0398.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JV3

7jv3


Resolution: 2.39→46.24 Å / SU ML: 0.3106 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.9506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 3032 5 %Random selection
Rwork0.1836 57626 --
obs0.1855 60658 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.35 Å2
Refinement stepCycle: LAST / Resolution: 2.39→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11706 0 145 138 11989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001512172
X-RAY DIFFRACTIONf_angle_d0.426716578
X-RAY DIFFRACTIONf_chiral_restr0.05391792
X-RAY DIFFRACTIONf_plane_restr0.00352270
X-RAY DIFFRACTIONf_dihedral_angle_d15.15064398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.430.30061290.2462452X-RAY DIFFRACTION91.1
2.43-2.470.30321360.24452575X-RAY DIFFRACTION100
2.47-2.510.30381390.23832640X-RAY DIFFRACTION100
2.51-2.560.29891370.24282618X-RAY DIFFRACTION99.93
2.56-2.610.32161370.24172603X-RAY DIFFRACTION99.96
2.61-2.660.28481400.23212659X-RAY DIFFRACTION100
2.66-2.720.29151390.232637X-RAY DIFFRACTION100
2.72-2.780.27231370.22362603X-RAY DIFFRACTION99.96
2.78-2.850.31421370.20972606X-RAY DIFFRACTION99.96
2.85-2.930.21991390.2112634X-RAY DIFFRACTION100
2.93-3.010.24241390.19372628X-RAY DIFFRACTION100
3.01-3.110.29011380.19542634X-RAY DIFFRACTION100
3.11-3.220.22661390.20482638X-RAY DIFFRACTION100
3.22-3.350.25031370.20842596X-RAY DIFFRACTION99.96
3.35-3.50.21231400.18492663X-RAY DIFFRACTION100
3.5-3.690.20381390.1682623X-RAY DIFFRACTION100
3.69-3.920.20371370.16772617X-RAY DIFFRACTION100
3.92-4.220.19251390.16792664X-RAY DIFFRACTION100
4.22-4.650.18431380.1522612X-RAY DIFFRACTION100
4.65-5.320.19761390.16832634X-RAY DIFFRACTION100
5.32-6.690.22711390.19272639X-RAY DIFFRACTION100
6.7-46.240.17111380.15122651X-RAY DIFFRACTION99.75

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