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- PDB-7s2k: Crystal structure of sulfonamide resistance enzyme Sul2 in comple... -

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Basic information

Entry
Database: PDB / ID: 7s2k
TitleCrystal structure of sulfonamide resistance enzyme Sul2 in complex with 7,8-dihydropteroate, magnesium, and pyrophosphate
ComponentsSul2
KeywordsTRANSFERASE / TIM barrel / alpha beta protein / antibiotic resistance / sulfonamides / structural genomics / CSGID / Center for Structural genomics of infectious diseases / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology7,8-DIHYDROPTEROATE / 4-AMINOBENZOIC ACID / PYROPHOSPHATE 2-
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsStogios, P.J. / Skarina, T. / Michalska, K. / Venkatesan, M. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nat Commun / Year: 2023
Title: Molecular mechanism of plasmid-borne resistance to sulfonamide antibiotics.
Authors: Venkatesan, M. / Fruci, M. / Verellen, L.A. / Skarina, T. / Mesa, N. / Flick, R. / Pham, C. / Mahadevan, R. / Stogios, P.J. / Savchenko, A.
History
DepositionSep 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 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: Sul2
B: Sul2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0979
Polymers57,0032
Non-polymers1,0947
Water6,684371
1
A: Sul2
hetero molecules

B: Sul2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0979
Polymers57,0032
Non-polymers1,0947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3440 Å2
ΔGint-37 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.730, 74.243, 67.989
Angle α, β, γ (deg.)90.000, 96.075, 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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sul2


Mass: 28501.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold

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Non-polymers , 7 types, 378 molecules

#2: Chemical ChemComp-78H / 7,8-DIHYDROPTEROATE / Dihydropteroate


Mass: 314.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PAB / 4-AMINOBENZOIC ACID / 4-Aminobenzoic acid


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: 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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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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 2% hexanediol, 0.1 M HEPES, pH 7.7, 2 mM PABA, 1 mM 6-hydroxymethyl-7,8-dihydropterin pyrophosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.74→30 Å / Num. obs: 45563 / % possible obs: 98 % / Redundancy: 4.6 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.034 / Net I/σ(I): 20.88
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 2261 / CC1/2: 0.968 / Rpim(I) all: 0.2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AJ0

1aj0


Resolution: 1.74→28.76 Å / SU ML: 0.1998 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 1999 4.39 %
Rwork0.1786 43535 -
obs0.1801 45534 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.07 Å2
Refinement stepCycle: LAST / Resolution: 1.74→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 73 371 4355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624052
X-RAY DIFFRACTIONf_angle_d1.01245504
X-RAY DIFFRACTIONf_chiral_restr0.0616627
X-RAY DIFFRACTIONf_plane_restr0.0088729
X-RAY DIFFRACTIONf_dihedral_angle_d15.53251481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.31441360.24022955X-RAY DIFFRACTION92.71
1.78-1.830.28161430.23813117X-RAY DIFFRACTION98.43
1.83-1.880.28851420.22543088X-RAY DIFFRACTION98.27
1.88-1.940.26661430.20623120X-RAY DIFFRACTION98.11
1.94-2.010.24141430.19573117X-RAY DIFFRACTION98.13
2.01-2.090.24431410.19543068X-RAY DIFFRACTION96.57
2.09-2.190.2271420.17623078X-RAY DIFFRACTION96.18
2.19-2.30.2141440.17073134X-RAY DIFFRACTION99.48
2.3-2.450.20551440.17363164X-RAY DIFFRACTION99.58
2.45-2.640.21561460.17253151X-RAY DIFFRACTION98.8
2.64-2.90.21481430.17123123X-RAY DIFFRACTION97.38
2.9-3.320.21351420.17163081X-RAY DIFFRACTION96.99
3.32-4.180.16781460.15323207X-RAY DIFFRACTION99.44
4.18-28.760.1991440.18293132X-RAY DIFFRACTION96.21
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)
14.273900135530.3463386807940.8870915307575.064522361050.7447541158924.52152366970.0614122931330.301690389196-0.275716032879-0.09711757743170.0161843932942-0.5539343491860.2352476434860.332748402284-0.04729253701780.287603257642-0.0331107364072-0.01298763821910.1732120316680.00398161167120.22948788598320.1042744536-4.1105760062913.0793978248
23.17997615668-0.164523067394-3.481523034873.023092222070.4304258726514.19154564383-0.03579780258670.0603886599065-0.0997215446174-0.05939351643410.008237716309760.1090308413540.501477807771-0.4126596313670.06940171708110.243637134164-0.0540173630921-0.0540528241870.1599547962810.004728498437990.1845552273959.45047282601-7.390948512527.95277407244
32.879973349971.102114152960.09110458852062.32813450409-0.9620986559254.40798655305-0.03279275115470.03387444814080.0773847444338-0.0987522509332-0.07380071029070.21780065865-0.00781650299643-0.1616722183890.1050602909240.2053221373920.00907239911843-0.03894655355430.108037931143-0.02613996921310.1651905048199.742740332645.499788970115.47371982292
42.624412903470.405626396165-0.4373169448346.497731092584.996660078267.54043715409-0.1573288313620.470726431749-0.89621789659-1.41461520304-0.0617108086941-0.7859861900860.2749025083340.7516296980590.2290147904770.595783275490.03322191534620.02446262453220.3302391036390.03241069960150.48458653203230.030744926411.8881109512-0.527184400722
56.136360422980.7647418385960.4048112950020.2261615783030.1022913737541.4007834830.08026378567970.1153055917440.133300638085-0.0721869124839-0.06767106788170.0767149069761-0.08547152747120.02181152697-0.001449730880010.2574840683930.0132453322145-0.02629489152150.0781308904551-0.003312601641290.16675620872918.958256308117.12694633125.35293881573
64.976610630370.105216289703-0.491937681140.6060659437551.253334017122.71523040799-0.0038581251942-0.044654864475-0.03702634610110.07449128785660.0744141882633-0.1189579548830.1037917809450.269294063416-0.06662941230670.252032700044-0.00526131507656-0.05073207722020.1303266133030.0135336981220.13907038705330.094045998112.410220069513.5112422633
76.3221809551-0.4202957125652.332898263810.273040138192-0.8708287249443.295240603620.0209663971802-0.1172948872320.07857123061450.06984320303790.00986712590052-0.001181231080120.1245812744410.0329712745491-0.02082798907130.253866138692-0.00789129065678-0.02567626434640.1201458529190.009499762193160.09525705597326.64452897168.2541274785120.2551513086
83.28364000921.358530041720.3755816498257.82079786795.242002257898.36757671217-0.0422428100779-0.3223206754510.3156663857440.4565511202260.03791807536850.2549951932970.10136106721-0.2314579675940.02339062628640.1532353414090.0304521471961-0.03867547086980.1652160635910.008835907939540.18243834845424.231440049812.267987901333.4808608854
98.0249176372-1.166349413320.7856571973065.097016523350.8575340540557.041679508790.0152098814875-0.2756276748660.1951817615650.1790147030130.01035851615280.0669320088173-0.374680033767-0.003767028756310.07903215569760.141495937828-0.003750520153490.01593877998940.165432076963-0.05480060942820.1027201785473.385351196853.5325143685637.2175519038
108.95402605642-5.37120110895.029644762714.80403790957-6.010069233688.708346030840.3411069331770.404573927577-0.934895595076-0.824992420185-0.002463243489870.5786150789880.734073428135-0.26263796579-0.3803311125510.25092664419-0.00565522181765-0.01380709659560.211996232727-0.08583843919580.2421976518556.49471078093-6.137238888332.8484420716
111.81817956407-0.2830710690220.2700170751920.5642981541980.2396160682980.1875174517260.00256713359962-0.224874445535-0.1169979605230.1357558884090.4595680046240.518626121251-0.142019848755-1.17637843482-0.6122699390730.267266157490.03952080910230.03072121491190.4244764869590.09382766636660.3011212842010.703551084143-1.5078888511645.8248639524
121.46919087007-0.668841978743-0.1839323053462.386192627271.278357375123.52822658564-0.100424991389-0.0496550755273-0.004867345716760.09353748556460.037914998274-0.136137431185-0.0431111181840.1776110300470.06446170754820.1286657749650.00131350594195-0.006733319487250.1213651280960.01615404056620.13712374733810.76556965393.9154340010348.3155823073
134.62347132945-2.958054191681.538774306648.19309018409-2.963770682916.76625918374-0.324660009904-0.649805581614-1.273602875541.015963110880.475865417261.013841654610.391609453006-0.981681086598-0.1145399829440.6040241273150.1068125858780.01194836803610.471424411861-0.04019598969490.383121484685-10.77971697999.8485517371154.4200536567
141.86062684125-0.01576606413541.687222943481.486878744680.1624581786652.65157323009-0.229100195221-0.07364545956380.212054911288-0.01838869898970.04953887013390.104386031108-0.396088482203-0.1987840595260.133855014610.2222232469170.0425176038807-0.01213017294720.147904376556-0.007310369573380.134565038319-5.659293456312.963762565239.057188876
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 60 )AA4 - 601 - 57
22chain 'A' and (resid 61 through 77 )AA61 - 7758 - 74
33chain 'A' and (resid 78 through 128 )AA78 - 12875 - 125
44chain 'A' and (resid 129 through 145 )AA129 - 145126 - 142
55chain 'A' and (resid 146 through 184 )AA146 - 184143 - 181
66chain 'A' and (resid 185 through 227 )AA185 - 227182 - 224
77chain 'A' and (resid 228 through 250 )AA228 - 250225 - 247
88chain 'A' and (resid 251 through 271 )AA251 - 271248 - 268
99chain 'B' and (resid 1 through 26 )BE1 - 261 - 17
1010chain 'B' and (resid 27 through 40 )BE27 - 4018 - 31
1111chain 'B' and (resid 41 through 60 )BE41 - 6032 - 51
1212chain 'B' and (resid 61 through 128 )BE61 - 12852 - 119
1313chain 'B' and (resid 129 through 145 )BE129 - 145120 - 136
1414chain 'B' and (resid 146 through 270 )BE146 - 270137 - 261

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