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- PDB-7k14: Ternary soak structure of alkanesulfonate monooxygenase MsuD from... -

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Basic information

Entry
Database: PDB / ID: 7k14
TitleTernary soak structure of alkanesulfonate monooxygenase MsuD from Pseudomonas fluorescens with FMN and methanesulfonate
ComponentsAlkanesulfonate monooxygenase
KeywordsFLAVOPROTEIN / OXIDOREDUCTASE / TIM barrel / flavin monooxygenase
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 monooxygenase / Luciferase-like domain superfamily
Similarity search - Domain/homology
methanesulfonic acid / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Alkanesulfonate monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLiew, J.J.M. / Dowling, D.P. / El Saudi, I.M.
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
DepositionSep 7, 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
E: Alkanesulfonate monooxygenase
F: Alkanesulfonate monooxygenase
G: Alkanesulfonate monooxygenase
H: Alkanesulfonate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,07223
Polymers354,2318
Non-polymers3,84115
Water28816
1
A: Alkanesulfonate monooxygenase
B: Alkanesulfonate monooxygenase
C: Alkanesulfonate monooxygenase
D: Alkanesulfonate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,32512
Polymers177,1164
Non-polymers2,2108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Alkanesulfonate monooxygenase
F: Alkanesulfonate monooxygenase
G: Alkanesulfonate monooxygenase
H: Alkanesulfonate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,74711
Polymers177,1164
Non-polymers1,6317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.000, 211.930, 94.350
Angle α, β, γ (deg.)90.000, 119.049, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 0 through 68 or (resid 69...
d_2ens_1(chain "B" and (resid 0 through 68 or (resid 69...
d_3ens_1(chain "C" and (resid 0 through 68 or (resid 69...
d_4ens_1(chain "D" and (resid 0 through 76 or resid 78...
d_5ens_1(chain "E" and (resid 0 through 68 or (resid 69...
d_6ens_1(chain "F" and (resid 0 through 68 or (resid 69...
d_7ens_1(chain "G" and (resid 0 through 68 or (resid 69...
d_8ens_1(chain "H" and (resid 0 through 68 or (resid 69...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERILEA1 - 77
d_12ens_1PROVALA79 - 210
d_13ens_1GLULEUA212 - 227
d_14ens_1VALHISA229 - 248
d_15ens_1ASNARGA282 - 297
d_16ens_1THRALAA302 - 356
d_21ens_1SERILED1 - 77
d_22ens_1PROVALD79 - 210
d_23ens_1GLULEUD212 - 227
d_24ens_1VALHISD231 - 250
d_25ens_1ASNARGD282 - 297
d_26ens_1THRALAD302 - 356
d_31ens_1SERILEG1 - 77
d_32ens_1PROVALG79 - 210
d_33ens_1GLULEUG212 - 227
d_34ens_1VALHISG229 - 248
d_35ens_1ASNARGG282 - 297
d_36ens_1THRALAG302 - 356
d_41ens_1SERILEJ1 - 77
d_42ens_1PROVALJ79 - 210
d_43ens_1GLULEUJ212 - 227
d_44ens_1VALHISJ229 - 248
d_45ens_1ASNARGJ282 - 297
d_46ens_1THRALAJ302 - 356
d_51ens_1SERILEM1 - 77
d_52ens_1PROVALM79 - 210
d_53ens_1GLULEUM214 - 229
d_54ens_1VALHISM231 - 250
d_55ens_1ASNARGM284 - 299
d_56ens_1THRALAM304 - 358
d_61ens_1SERILEP1 - 77
d_62ens_1PROVALP79 - 210
d_63ens_1GLULEUP212 - 227
d_64ens_1VALHISP229 - 248
d_65ens_1ASNARGP250 - 265
d_66ens_1THRALAP267 - 321
d_71ens_1SERILER1 - 77
d_72ens_1PROVALR79 - 210
d_73ens_1GLULEUR212 - 227
d_74ens_1VALHISR229 - 248
d_75ens_1ASNARGR272 - 287
d_76ens_1THRALAR292 - 346
d_81ens_1SERILEU1 - 77
d_82ens_1PROVALU79 - 210
d_83ens_1GLULEUU212 - 227
d_84ens_1VALHISU229 - 248
d_85ens_1ASNARGU260 - 275
d_86ens_1THRALAU280 - 334

NCS oper:
IDCodeMatrixVector
1given(0.278812456974, -0.166111599817, 0.945870260788), (-0.175807348319, -0.977110835639, -0.119775586636), (0.944116195239, -0.132896016807, -0.301634312709)-84.726298116, -10.9892337571, 112.548462097
2given(-0.965818742186, 0.259196109048, -0.00339621787935), (0.259149863783, 0.965781832891, 0.0103343775516), (0.00595863597921, 0.00910100612732, -0.999940831422)-174.696422091, 22.745888813, 44.5787219671
3given(-0.316660862118, -0.0867507548693, -0.944563499682), (-0.0955078787116, -0.987832141791, 0.122743247262), (-0.943718254304, 0.12908123866, 0.304522397073)-95.9475070793, -9.2971507818, -68.5950413238
4given(-0.903523579269, 0.327403577184, -0.276499619082), (-0.333923805513, -0.942279412936, -0.0245845493912), (-0.268588968159, 0.0701170849661, 0.960699516279)-121.059275573, -77.6495749845, -65.6552462407
5given(-0.565524761802, -0.128687982671, -0.814629453742), (0.0742308478648, 0.975799907358, -0.205680144949), (0.821383908421, -0.176787850027, -0.542286392111)-78.6902281022, -39.0595756196, 64.79228839
6given(0.956312785147, 0.0765380038146, 0.282148526376), (0.0748449359038, -0.997053821803, 0.0167902351612), (0.282602357622, 0.00506067182167, -0.95922379926)31.8250028028, -42.259737987, 26.0702928916
7given(0.507943674867, -0.27347006175, 0.816827612467), (0.215103243558, 0.958493706615, 0.18713740671), (-0.834100604108, 0.0806470068001, 0.545685112973)-19.5670534139, -35.4767446698, -106.681365666

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 44278.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf0-1 / Gene: msuD, ssuD, Pfl01_3916 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3K9A1, alkanesulfonate monooxygenase

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Non-polymers , 5 types, 31 molecules

#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-03S / methanesulfonic acid


Mass: 96.106 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH4O3S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 47 %
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: 2.75→82.21 Å / Num. obs: 82800 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 81.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.037 / Rrim(I) all: 0.091 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
2.75-2.825.959870.7197
2.82-2.95.8259890.788199.1
2.9-2.985.8857880.8621
2.98-3.075.4455330.9011
3.07-3.186.2154890.9511
3.18-3.296.1952930.9671
3.29-3.416.3151090.9811
3.41-3.556.1549370.9851
3.55-3.715.8147320.9891
3.71-3.895.9645150.9931
3.89-4.15.7143180.9931
4.1-4.355.3140540.9941
4.35-4.655.2137590.9951
4.65-5.025.9435720.9951
5.02-5.55.832770.9961
5.5-6.155.9629620.9961
6.15-7.15.6326180.9961
7.1-8.75.221990.9981
8.7-12.35.5817060.9981
12.3-82.219620.997198.2

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Processing

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

7jv3


Resolution: 2.75→81.16 Å / SU ML: 0.4162 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.0733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Rfree test set was transferred from 7JV3 (unliganded MsuD) due to similar unit cell values
RfactorNum. reflection% reflection
Rfree0.2144 4123 4.98 %
Rwork0.1715 78662 -
obs0.1736 82785 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.63 Å2
Refinement stepCycle: LAST / Resolution: 2.75→81.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21497 0 249 16 21762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005722302
X-RAY DIFFRACTIONf_angle_d0.761830416
X-RAY DIFFRACTIONf_chiral_restr0.06913320
X-RAY DIFFRACTIONf_plane_restr0.00574138
X-RAY DIFFRACTIONf_dihedral_angle_d15.50947912
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.322438970378
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.310806008188
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.344502341863
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.270331764649
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.431809611925
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.327846889046
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.366501060535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.780.34341300.3162571X-RAY DIFFRACTION94.54
2.78-2.820.32961490.29692686X-RAY DIFFRACTION99.58
2.82-2.850.37191330.30072776X-RAY DIFFRACTION99.66
2.85-2.890.34651520.27442686X-RAY DIFFRACTION99.3
2.89-2.930.28991430.2612685X-RAY DIFFRACTION99.3
2.93-2.970.25381380.24452726X-RAY DIFFRACTION99.03
2.97-3.020.28461410.24112702X-RAY DIFFRACTION98.68
3.02-3.060.30731350.24262624X-RAY DIFFRACTION96.5
3.06-3.110.29421490.22452698X-RAY DIFFRACTION99.55
3.11-3.170.28571450.2212736X-RAY DIFFRACTION99.62
3.17-3.220.24691350.21482744X-RAY DIFFRACTION99.58
3.22-3.290.2581350.21812710X-RAY DIFFRACTION99.51
3.29-3.350.24131560.20462724X-RAY DIFFRACTION99.55
3.35-3.430.25431310.20062707X-RAY DIFFRACTION99.51
3.43-3.510.23321480.19952729X-RAY DIFFRACTION99.76
3.51-3.590.24261400.19482722X-RAY DIFFRACTION99.9
3.59-3.690.21331510.17662739X-RAY DIFFRACTION99.9
3.69-3.80.22361340.16842742X-RAY DIFFRACTION99.65
3.8-3.920.19921540.16042725X-RAY DIFFRACTION99.72
3.92-4.060.20741340.15872727X-RAY DIFFRACTION99.76
4.06-4.220.18151400.15432692X-RAY DIFFRACTION98.95
4.22-4.420.17681490.14062686X-RAY DIFFRACTION98.68
4.42-4.650.18581450.13642708X-RAY DIFFRACTION98.18
4.65-4.940.18251390.13842755X-RAY DIFFRACTION99.9
4.94-5.320.18681480.13792704X-RAY DIFFRACTION99.62
5.32-5.860.20011420.15222757X-RAY DIFFRACTION99.62
5.86-6.70.19391430.16262730X-RAY DIFFRACTION99.52
6.7-8.450.19231430.15692713X-RAY DIFFRACTION98.65
8.45-81.160.2081410.16062758X-RAY DIFFRACTION98.54
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.48853984345-0.5679935788360.8330141954971.528429083-0.1026132070692.250786357730.01636494420020.6140438955390.162436832207-0.0721748427104-0.336674408158-0.453997913697-0.09335930940681.049446817750.1828854973150.561795638379-0.04849529569730.1074063699970.9498222932250.1794451333380.74517237666630.0692574376-11.008939563520.4788710696
23.503820713350.07394341560070.700690635571.689876461760.5790977788642.345831396430.10467673062-0.5386894251160.1405948061510.452010913492-0.295325313481-0.0745722524513-0.293091752336-0.04067795777180.1945816568871.03075917553-0.173720846207-0.02137098234570.5307397470760.003952692215950.62876125673913.04344992638.7939415662247.1725468458
31.615416110920.4701124596590.0726558495890.9565414265550.09664362347973.2274954349-0.0250323367435-0.2980397294580.2953427132220.102611267003-0.1302079388650.331970921731-0.261250008438-0.8290067720330.143730429840.6594961159310.05113146967740.1017890018990.681741018385-0.119570405660.734364500989-21.8617223188-4.1654401972323.3888865604
43.34569749684-0.9277704632581.013409039791.87894550916-0.8434049728542.8571802926-0.1085280038460.7019514493890.271675830907-0.298727289279-0.330522712269-0.123933835414-0.4845115164320.3854842239820.3146891044170.841265418979-0.0469150853831-0.01688012919020.5312130527940.09795584321420.557622592333-0.27323802714510.5809320427-3.24732873364
51.165856107580.349843473353-0.08017523319451.181099520350.105014258492.567732985730.126817082748-0.177267131999-0.06840299164910.160400876756-0.160968414343-0.2487377336360.01970460458610.3337349055670.03839366278280.581629804266-0.0330163690156-0.04932274296210.4863532059480.03670070393120.629137213256-24.1924417261-35.5448084532-12.3617792906
64.024936467720.0969042747167-0.07769631268311.804853802630.5877327731722.875742904190.0948835656370.404358701523-0.208167065449-0.251812012983-0.15078731032-0.05776561370240.2228676560820.008947061024960.05074496364880.7281759123160.103166254008-0.008169842958910.4412745457660.004050887161020.661920181793-31.8786666542-57.3667850478-40.5437449318
72.2157380538-0.138876872161-0.6393590632761.55748722728-0.3076777285782.964382342720.2411809637540.5525224917620.0119251540927-0.07517463136670.1083171478740.758105319650.0287924609855-1.20028326914-0.2543676919810.5605826937650.0464625795579-0.0519780028541.076631817470.1501180378311.09186804681-72.3511735944-46.0838361047-28.8323648771
82.462978631730.602011002325-0.04973689081432.31758070577-0.7259085201482.835902372180.239428980201-0.316392848750.1082895648480.393652552347-0.1643677216710.1955398831480.0510940391737-0.214966042332-0.08409625523090.770297878389-0.1668947843510.02550125969630.5242291247250.05732016842350.591671508186-56.3785441542-60.31162913361.08209428429
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11chain 'A'AA - C0 - 501
22chain 'B'BD - F0 - 501
33chain 'C'CG - I0 - 501
44chain 'D'DJ - L0 - 501
55chain 'E'EM - O0 - 501
66chain 'F'FP - Q0 - 401
77chain 'G'GR - T0 - 501
88chain 'H'HU - W0 - 501

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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