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- PDB-7s2j: Crystal structure of sulfonamide resistance enzyme Sul2 apoenzyme -

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Basic information

Entry
Database: PDB / ID: 7s2j
TitleCrystal structure of sulfonamide resistance enzyme Sul2 apoenzyme
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 / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
C: Sul2
D: Sul2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,68526
Polymers114,0064
Non-polymers1,67922
Water20,3031127
1
A: Sul2
hetero molecules

C: Sul2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,80513
Polymers57,0032
Non-polymers80211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area4350 Å2
ΔGint-110 kcal/mol
Surface area22910 Å2
MethodPISA
2
B: Sul2
D: Sul2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,88013
Polymers57,0032
Non-polymers87711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-118 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.819, 143.293, 85.893
Angle α, β, γ (deg.)90.000, 90.506, 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, 4 molecules ABCD

#1: Protein
Sul2


Mass: 28501.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: Sul2 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold

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Non-polymers , 5 types, 1149 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1127 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.77 %
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 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 81585 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.63 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Net I/σ(I): 19.34
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 4084 / CC1/2: 0.711 / Rpim(I) all: 0.328 / % possible all: 99.3

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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
Resolution: 1.85→42.94 Å / SU ML: 0.2244 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 3896 2.43 %
Rwork0.1612 156647 -
obs0.1623 81545 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.8 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7920 0 89 1127 9136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00628179
X-RAY DIFFRACTIONf_angle_d0.895211105
X-RAY DIFFRACTIONf_chiral_restr0.05721270
X-RAY DIFFRACTIONf_plane_restr0.00841470
X-RAY DIFFRACTIONf_dihedral_angle_d14.17212990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.34391280.25685360X-RAY DIFFRACTION94.69
1.87-1.890.25121430.24735628X-RAY DIFFRACTION98.45
1.89-1.920.31121390.23655371X-RAY DIFFRACTION95.51
1.92-1.950.27631360.22315574X-RAY DIFFRACTION98.4
1.95-1.970.24381490.2155648X-RAY DIFFRACTION99.14
1.97-20.24331440.20515682X-RAY DIFFRACTION99.13
2-2.030.23691330.19885490X-RAY DIFFRACTION99.22
2.03-2.070.26351400.19835680X-RAY DIFFRACTION99.08
2.07-2.10.2481440.20155691X-RAY DIFFRACTION99.1
2.1-2.140.21821370.17475540X-RAY DIFFRACTION99.14
2.14-2.180.22821480.17565566X-RAY DIFFRACTION98.4
2.18-2.230.21391340.17065667X-RAY DIFFRACTION98.57
2.23-2.270.26481490.17715471X-RAY DIFFRACTION98.39
2.28-2.330.25831380.17065622X-RAY DIFFRACTION97.51
2.33-2.390.18331410.17335580X-RAY DIFFRACTION99.39
2.39-2.450.22671430.16525623X-RAY DIFFRACTION99.17
2.45-2.520.22341410.17615668X-RAY DIFFRACTION99.32
2.52-2.60.21031360.16175663X-RAY DIFFRACTION99.54
2.6-2.70.23831360.16535637X-RAY DIFFRACTION99.43
2.7-2.810.23431430.16075602X-RAY DIFFRACTION99.07
2.81-2.930.2191330.16935555X-RAY DIFFRACTION98.36
2.93-3.090.19631380.16215582X-RAY DIFFRACTION98.23
3.09-3.280.17111420.15325655X-RAY DIFFRACTION99.57
3.28-3.530.18281400.13775619X-RAY DIFFRACTION99.46
3.53-3.890.20321450.13535667X-RAY DIFFRACTION99.64
3.89-4.450.16021340.12165570X-RAY DIFFRACTION97.96
4.45-5.610.1641360.14155643X-RAY DIFFRACTION99.66
5.61-42.940.19011260.15695593X-RAY DIFFRACTION98.48
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.797011471010.902709857174-0.2198376952511.171452482340.8259078838371.25899818037-0.134036009614-0.745285714193-0.4293293824941.068855107910.2857081648590.1571628458210.50112709047-0.276726159680.00306392271030.6725048151580.01520411376980.04984879327090.3916659632820.09038688939830.30774163044913.18544462556.483047418911.3048003126
21.286131559430.688721176279-0.06590488435323.270855931921.702428698912.359480015310.0815321119534-0.184552782704-0.1748563211240.880653813272-0.2167168150930.2761019208950.603835705451-0.1318038679870.01204177626890.354494795917-0.055733683220.07648187916650.248562548623-0.01359081701160.2530359878647.497346387653.221460005092.21232050165
30.827082443091-0.2543572442290.02782931779930.5140272653620.3787315305380.38238264133-0.1810224135860.127081391751-0.730615489686-0.296664498549-0.0248278941311-0.324378839450.4447846014690.452942634075-0.00755655038370.305815992590.05454170039190.05662732665870.3707616784440.004580216895280.41846327414227.78385375783.22665079967-10.2667243189
40.6550811273390.4467724978850.4998604055792.196840438181.894886563992.26465148645-0.0212682109263-0.09270208383660.1403635775190.05398659172780.0565514195111-0.0312498760103-0.09442061128290.190243832610.01050889365910.167769929491-0.01956339798020.005530101244050.235649908162-0.007138530633050.1610759538519.031617512417.7687039812-3.61599549952
51.31981894704-0.6178611670040.5512168835831.028248688230.4513248763751.351198775820.08270343023710.157198871938-0.018353143872-0.108668301861-0.0702149893776-0.129776556363-0.137906883505-0.01604313605413.29372706982E-70.1983681164410.03418216660330.01365560485530.207408904796-0.00229367797450.208067699032.0208772317612.737773219-55.3215224218
60.382663349168-0.591397104218-0.1860804603791.288115681030.136489237470.9315967384660.1227621874180.100519694114-0.146470982909-0.0970652016344-0.00199180238331-0.5057067167930.00881520827160.08994014230341.02400273703E-70.2343804700140.00678990054908-0.03449344234990.2323438356630.00608170892880.2539253804610.29532192272913.3856231586-54.3348817359
70.837263376089-0.429764432354-0.4557582038711.3272865558-0.5046018232180.7295558943760.0384782818543-0.0367471298491-0.04901420685980.1039317882520.03753922048590.158936602276-0.155345359549-0.2049132700421.01135356735E-70.2570863727010.0232518444803-0.01549526647060.256154704730.01913462603660.229150488464-6.4697793142420.1432114216-49.0323205627
80.461185063611-0.206525785623-0.03413693965550.217870835744-0.2007110853910.6884928705110.00703834824622-0.07437039080020.3342016113560.1386404767650.06374663620580.0720179990489-0.176084361146-0.05058626308061.66541600558E-80.2407206709180.03215895775220.01389988027890.271956121017-0.009326706685330.274571016184-5.8366118247516.6617573653-36.6291269986
94.053371775670.003312238716140.0859400080570.000483648442501-0.008077547906990.715059504122-0.00276569046126-0.3553678656060.8618312614040.2405371603910.0786027505231-0.162499879288-0.4557863282550.180843550656-0.01382008233720.30547304299-0.0116668323981-0.01729931642570.266857908521-0.02802738260190.32224902361614.359696420713.431691688-31.6558763377
100.7763096205970.1336868471230.7081637550111.39512000858-0.2893328380671.323627000340.00464072581472-0.03966891477-0.118859901440.1106617632960.05037478138080.003163283265820.1150870066430.0439434285455-4.97986290736E-80.2026232500660.0131024199825-0.02031270447930.2391514729840.0002398846042340.2104968803653.75981119965.41462948684-31.7664144658
111.44189188712-0.1481414274871.245635352771.508011315580.3951085406461.23986966231-0.04875173915350.5531133249620.0930207692206-0.2361839041490.0674880336234-0.3833206753120.1327114745950.2377107629181.14791800702E-60.2456073750550.02090583479450.01020280401390.2400683038740.0201809167150.28314834788211.57919385342.07694236928-46.5858504715
120.384386547299-0.1881801239970.1573260446480.2023818123630.03171751605140.1215036787630.0175934324851-0.0535511601956-0.137305088957-0.120728015249-0.0263037487075-0.03133746404750.1696494101750.0215960206701-3.28139463869E-60.2403670708940.00848743836170.004062571012790.218363622875-0.01442234090930.2580977781144.29033530328-1.76866250648-46.9063428021
130.711889108424-0.19665705971-0.077678769280.7135162553460.6061869826580.503563739183-0.271187326904-0.389967885057-0.29666409610.01889194830950.1541980480640.6672830698390.265336613085-0.3218661726660.005456126515640.3130629582820.01814374259630.04165310375750.3115368345730.02110851927480.345424172967-1.88325131332-12.019930557-49.9906236968
141.842183264430.1906992748740.878393922342.23345852216-0.1767950576830.4646903582090.121869316717-0.0158952217695-0.00119375329759-0.129752135854-0.0453817078035-0.138011243946-0.660135310828-0.0607509243765-0.002115820369410.24116766226-0.0165438577696-0.01223339410210.2057473821210.000585259416650.1689153976996.68328554363-34.4800251249-23.8254663168
150.8920406955360.017143964856-0.01493814267463.130925660451.225918636281.845910934630.02640922385530.04761753434570.142706870697-0.375218645921-0.1775592445270.181949654471-0.120267544254-0.0575311049509-0.001813826109270.1545341037650.0136724047627-0.03579786880980.180819585954-0.006115427825920.1947020179051.58991095068-25.9876943536-23.9430026763
161.3650920976-0.376122111885-0.2525954999780.4286540319930.4408827455550.489937552237-0.1418630405940.6772108825831.006374808490.06807575006640.353353903274-1.31326359651-0.5329550578641.024158764420.09562638666720.40609192603-0.191807959816-0.08465230135190.5474813936720.08425385598220.79339293159222.028578495-15.5043703626-16.7388070685
170.7606269968590.8130336226840.208362118392.34250444476-0.7123767354731.61303517366-0.0334406854735-0.1412726857460.03135559499720.730395436506-0.150989079472-0.482651303735-0.201392568670.227023986705-0.008748505158470.261745548464-0.0569658361215-0.09430752380040.215990440846-0.007420448531680.2876137590613.1906205571-19.6300049699-8.05116133126
180.9721722665840.3722341105780.324064654711.01269179103-0.6867614459010.8395437331180.03732459923020.0716549925486-0.6056543224990.0914077788213-0.384676809933-0.201302652940.06795400140240.331480409216-0.0004339815293610.268697369662-0.0158096164405-0.0112828873880.3707468707210.06323964140850.36267722943819.8721226682-34.6326395421-14.3863730499
190.5229944931380.2190526885770.1196575529150.362256007718-0.2628303168420.334389174002-0.0192459426674-0.141882670018-0.1183355357010.199254410907-0.146579139395-0.210657254588-0.04553627480650.108481509521-1.39139868691E-70.275082965315-0.00532572039721-0.03005957035430.3018729792280.05190657406460.23698087095212.7283002479-36.2340617269-10.2278700075
200.552097410815-0.04356203936840.09055583463151.190701596970.1154172278880.325249268641-0.133007655301-0.6399140868740.05745665142980.3806347729290.381296290290.746258622730.215722711934-0.411052648403-0.01807779637340.28803939270.0694193477480.04120823339370.409357623950.07151317277680.3765159569957.37928958854-44.8977494293-1.55551044967
211.637989203680.469723096359-0.8154218271164.844462537360.6502356106052.000526199590.02564766349170.2978203699340.147078568623-0.754164681230.102322240389-0.174287520794-0.135890772922-0.0307150040070.0004256300193560.4301528590950.05597645707350.08378181405730.3399396957530.01365461379380.31026217607519.7862756404-26.6167310086-68.4123923382
220.445643260526-0.2406758721770.01232939892660.236771327062-0.06663027884490.292989652150.008707812601690.589017726679-1.15102763474-0.194332574307-0.03814998615461.723716261080.678477224853-1.278122878150.03355372534660.823742995448-0.07324767741710.004242157520360.662119459233-0.1306414127520.860399601927-0.209964158735-36.4377555558-60.7861546366
231.15455130725-0.863409151959-0.09673968140793.96317914231.144992145351.34039815874-0.0499406040143-0.08438328724130.010682603169-0.00295384842290.02982878151920.1240981213990.132037137375-0.02815342312920.00112016725280.2784496583060.02705611239830.01091958859880.2263216458950.01599012352940.20024846508810.2688677795-24.0064824628-52.9798791
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 26 )AA3 - 261 - 24
22chain 'A' and (resid 27 through 128 )AA27 - 12825 - 126
33chain 'A' and (resid 129 through 145 )AA129 - 145127 - 143
44chain 'A' and (resid 146 through 269 )AA146 - 269144 - 267
55chain 'B' and (resid 3 through 26 )BB3 - 261 - 24
66chain 'B' and (resid 27 through 60 )BB27 - 6025 - 58
77chain 'B' and (resid 61 through 98 )BB61 - 9859 - 96
88chain 'B' and (resid 99 through 128 )BB99 - 12897 - 126
99chain 'B' and (resid 129 through 145 )BB129 - 145127 - 143
1010chain 'B' and (resid 146 through 202 )BB146 - 202144 - 200
1111chain 'B' and (resid 203 through 227 )BB203 - 227201 - 225
1212chain 'B' and (resid 228 through 250 )BB228 - 250226 - 248
1313chain 'B' and (resid 251 through 269 )BB251 - 269249 - 267
1414chain 'C' and (resid 1 through 26 )CC1 - 261 - 26
1515chain 'C' and (resid 27 through 128 )CC27 - 12827 - 128
1616chain 'C' and (resid 129 through 145 )CC129 - 145129 - 145
1717chain 'C' and (resid 146 through 202 )CC146 - 202146 - 202
1818chain 'C' and (resid 203 through 227 )CC203 - 227203 - 227
1919chain 'C' and (resid 228 through 250 )CC228 - 250228 - 250
2020chain 'C' and (resid 251 through 270 )CC251 - 270251 - 270
2121chain 'D' and (resid 2 through 128 )DD2 - 1281 - 127
2222chain 'D' and (resid 129 through 145 )DD129 - 145128 - 144
2323chain 'D' and (resid 146 through 270 )DD146 - 270145 - 269

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