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- PDB-7s2m: Crystal structure of sulfonamide resistance enzyme Sul3 in comple... -

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Basic information

Entry
Database: PDB / ID: 7s2m
TitleCrystal structure of sulfonamide resistance enzyme Sul3 in complex with 6-hydroxymethylpterin
ComponentsSul3
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 / homology6-HYDROXYMETHYLPTERIN
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsStogios, P.J. / Skarina, T. / Venkatesan, M. / Michalska, K. / Mesa, N. / 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: Sul3
B: Sul3
C: Sul3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9386
Polymers87,3593
Non-polymers5793
Water6,233346
1
A: Sul3
C: Sul3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6254
Polymers58,2392
Non-polymers3862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-14 kcal/mol
Surface area22230 Å2
MethodPISA
2
B: Sul3
hetero molecules

B: Sul3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6254
Polymers58,2392
Non-polymers3862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554-y,-x,-z-1/31
Buried area2880 Å2
ΔGint-16 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.087, 50.087, 583.049
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z

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Components

#1: Protein Sul3


Mass: 29119.564 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: Sul3 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HHR / 6-HYDROXYMETHYLPTERIN


Mass: 193.163 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H7N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M calcium chloride, 0.05 M magnesium chloride, 20% w/v PEG3350, 6-hydroxymethylpterin
PH range: 7

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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: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.36→30 Å / Num. obs: 35008 / % possible obs: 98.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.98 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.05 / Net I/σ(I): 25.39
Reflection shellResolution: 2.36→2.4 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 1 / Num. unique obs: 1497 / CC1/2: 0.749 / Rpim(I) all: 0.457 / % possible all: 86.7

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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: 2.42→30 Å / SU ML: 0.336 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3003 1338 5 %
Rwork0.2477 25446 -
obs0.2503 26784 81.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.57 Å2
Refinement stepCycle: LAST / Resolution: 2.42→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5886 0 42 346 6274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00246039
X-RAY DIFFRACTIONf_angle_d0.54588136
X-RAY DIFFRACTIONf_chiral_restr0.0431940
X-RAY DIFFRACTIONf_plane_restr0.0051031
X-RAY DIFFRACTIONf_dihedral_angle_d24.19722264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.510.3442440.3371837X-RAY DIFFRACTION26.45
2.51-2.610.3549630.33511233X-RAY DIFFRACTION40.82
2.61-2.730.3689960.32971834X-RAY DIFFRACTION60.29
2.73-2.870.35181430.31422774X-RAY DIFFRACTION88.66
2.87-3.050.34131590.29133056X-RAY DIFFRACTION99.88
3.05-3.290.32641620.27213118X-RAY DIFFRACTION99.45
3.29-3.620.31921660.2483151X-RAY DIFFRACTION99.61
3.62-4.140.28231660.21383102X-RAY DIFFRACTION99.33
4.14-5.210.25851650.20613094X-RAY DIFFRACTION98.52
5.21-30.040.26421740.22233247X-RAY DIFFRACTION97.71
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)
14.67522310098-1.354739241390.8313396891761.44923991831-0.9814671783862.98667229398-0.0976103580566-0.1812843080910.3162872143510.1788290400070.0648208564928-0.180759112363-0.1248158879870.01799858136660.08493578072830.398496350355-0.2810143467060.03063367426850.126627261656-0.1369657819320.08632012526863.25113713137-9.21020839851-41.1211454373
22.012233428631.82393657871.081367087832.714662082250.7207072997933.54550613625-0.003382779476480.176458621582-0.452805851643-0.3886223493230.219126209965-0.3449539192320.504837066451-0.0744509878519-0.1285982361970.690351281134-0.2164917241850.09426694264230.07109149430890.06203727757770.465861232638-3.93339209409-21.7652881602-43.259824157
31.697279439210.8153231942591.106548167233.249576558490.4419075841822.845054611030.07979562367090.326814106033-0.29892708057-0.6174309879630.277285200626-0.1851931064770.1155024558680.109515788407-0.4400569862480.420227424916-0.175914287857-0.03155129733060.0753248956963-0.08183004528010.361507324709-0.157326729653-13.2778055333-51.9175306161
40.1955674753450.0522510379884-0.05658557811330.27165525759-0.1177505279170.09656083804190.0978645323890.0130398837088-0.0364241472995-0.132070452854-0.02138093646170.1345967688210.0312972085108-0.05330246582840.09832232835590.774133199596-0.581649419908-0.047492342717-0.143513709306-0.2862935171530.215437700846-6.65216794304-6.34456027476-53.4222652224
52.542621418722.052272771340.2201042291912.89756189845-0.5758051796410.4751760368110.05523795759140.187403098539-0.347963826996-0.3002512623380.0768313634938-0.157475067183-0.02210067210880.02942420661180.02429754059860.597943324144-0.204422072697-0.002966900587880.08017464913530.01280808327950.1066126889959.70326430453-0.776239906372-55.599338346
60.0845640515696-0.005974338408530.06091827936890.04447976188410.02414711030240.02311736487890.09441294538080.02406168706470.00949250176423-0.01543540433410.03534110886160.00541417796532-0.0655439878720.008139169785460.1721890261260.68842087098-0.740303082412-0.13448946142-0.627247767038-0.3225414997370.030273595607213.21193284393.84964324569-52.1690264423
70.6272443904510.2131108223690.1851209163970.1536499760920.1609757572210.451771674109-0.02547839209710.0590626547332-0.2057496427260.1131797301120.0587700676405-0.1015768020360.09627166409990.091665080555-0.1034763543890.779643081812-0.2335351133060.08390928945710.0117247352281-0.2049589288930.11859558406416.1363969656-10.6514315541-44.2518921581
80.0684539162852-0.01014217618690.02032495415150.0276613286305-0.01969188993830.229684239163-0.02630770547460.003290073633470.01829513692740.0206276872303-0.004662878232920.01083741440520.004591578380730.0196052040569-0.06153085535970.695154991375-0.2499518139550.06550683040080.01775420263850.0204630077615-0.029416901062813.0105811338-5.64982973894-38.0786440532
90.845382926665-0.58472953421.116968737480.420821435009-0.5916770834263.48923184047-0.0697048783417-0.003991835625840.0876279182740.0906543093888-0.01413650290220.00272068251675-0.1630429697430.08089887663430.0226939786280.519087960481-0.0662379322320.0426982400867-0.04270311384330.09114175058030.042367037669810.7745687543-7.39409110786-27.9189006343
101.887115962391.654394292021.303342067582.577179284111.420330469263.86772447396-0.02949313204910.10842871496-0.0888040819968-0.1947584524660.201030288868-0.01052970036870.097402012165-0.0297530078899-0.09866677624940.532403942471-0.432579091113-0.01977413130180.4701755583030.008031126913610.10695065585124.22126502372.02048463228-85.8421188702
115.51825997061-1.514867667875.345257091991.31240664228-1.264874426746.320105439720.695726171116-0.383845049393-0.6903536497130.382347843105-0.147089445846-0.4881939675530.4828838588540.307717758437-0.4679317175680.73511848531-0.54824534602-0.04756355726110.755047865255-0.09352907600580.52609378597837.2000574724-2.8123801335-87.2408113576
123.22649130139-0.3117529067241.944709009342.851877780620.5774763448224.077637858690.381927838945-0.926741776643-0.2721120172440.8053079869840.102959953208-0.6332017081710.669781600604-0.255341688807-0.4279369763960.729185425042-0.356449131758-0.2203649262290.629443983716-0.1158183300710.51559749228630.386995778-0.649009984675-74.7448815137
135.576313168922.357841758311.775340714644.013854740462.750838132314.901470529280.0136869668896-0.1278975874820.03543470485560.2182340493610.00325607617654-0.401245242645-0.1095554860890.430127538841-0.01448644566170.476077507239-0.276276675666-0.1779621729550.487385746659-0.2168464215680.51368236221836.81183889597.00328654679-78.8031917911
140.06175147316710.00959797914686-0.1261713277940.548890630566-0.7825404242121.34041222632-0.06902620618880.08038912902860.06439648164320.0755096803480.0714509160039-0.230759394931-0.311338299260.355134585046-0.01286667261990.489431105877-0.5095137199-0.2842748415780.425576570804-0.1723877187640.072036916895127.52791337819.42293795195-75.3247991526
150.701799648086-0.1247926237880.5714592546120.1506411164420.3416737734672.048867955980.0328757412874-0.0611481742394-0.1250154164290.156254748545-0.1160977067920.006620255625920.240354181061-0.226148624897-0.02817797160290.536916653911-0.546760402931-0.147917940040.166325048989-0.03040873344360.026603303529316.63889648115.1519145792-69.1772526245
160.4699047823940.09493541286210.08021921352140.416690053267-0.009816646080540.8180659003820.0482464478731-0.0009802921199130.05692833407060.1050628043620.00595989471969-0.00599484142983-0.125754223381-0.03088743956290.1032487685790.568595188444-0.451477042762-0.256517293195-0.0369830018364-0.02695086861510.123013232077.166755823244.06722504871-74.5919880526
171.729633804490.581332070160.2743989381450.581422291442-0.1019684037570.754071759454-0.04074013218950.294014897463-0.495016400451-0.1845182165850.100256237405-0.2547645727610.2122897645390.0540772508681-0.239908133150.367970812903-0.281793706928-0.0417158994430.19077018509-0.1418904819590.15947740366814.3384576049-7.65388092107-84.9948771923
180.1271996961550.124169409250.09770293048680.2149089069830.1204026904640.333211059172-0.03532241803780.0647213340225-0.00370226196234-0.07624519924710.04419709233670.014577745743-0.02350853697040.01323280489310.04862014066280.473143049219-0.486717801317-0.1187278540020.361711541423-0.02030181264790.037927353135413.5543039617-0.0418740392903-93.9875328992
194.59234309536-2.08568265853-0.5487015296814.27961889282.126077211382.962771779630.0961858888991-0.00599502990231-0.162390171373-0.0562360845818-0.04308016405650.9076886444240.2869112188320.0353706279059-0.0209852940730.6415351079450.3319177346980.04388388090980.215991766957-0.09562108897540.38108415455829.8410164727-23.3149523551-24.2833439019
201.40840881649-1.326447472330.09006202867192.981272372110.3770741843710.3373593807-0.151855518733-0.132909981876-0.3655318112470.3917987135870.1088197352150.1959559637480.2755497268070.01200434292880.1186512493590.9603624164010.354672585540.3662389482630.269934030266-0.08540942585170.51093195116633.6661562822-31.3256373994-22.1367602763
210.2456612863980.07047099834420.273032723981.0604118266-0.1190481491240.584649317609-0.112694274373-0.0383299118315-0.0565045043473-0.04440972293390.0190079385478-0.1619061599250.1299388900160.158906325593-0.02860924871620.6660819718650.6964674645910.2382054259370.3218544590060.1336410919590.37081216520337.4623125154-20.0521018427-10.4643532809
220.578365299768-0.3577245620260.3029217957760.966668593081-0.517878670550.623572828092-0.0952735331079-0.02496704696230.06300484989190.0179700699855-0.0415010710054-0.166579975891-0.02381206081550.1060630579610.1472606061310.699110157250.467968647063-0.09368554617870.1687134413940.2191842254130.055404229802630.8599031989-6.16211251867-10.8556632645
230.986788611932-1.29032632307-0.761198490382.20244281364-0.004240749343982.52371721842-0.139441901070.0811753262602-0.466932473069-0.223478965796-0.007271588664940.1996930369790.302121438878-0.2133984222110.1585346645460.7169381684830.0795126945490.2044970745610.1234205416740.02042359076620.1493397606419.183047255-14.0618889801-20.2907823352
240.087884091332-0.0329545396558-0.01708633201190.127539777028-0.1339404796750.201037464786-0.08892244072310.0145539490356-0.0480250502186-0.04066879623990.0242566628312-0.01747140850780.06041440439310.0123864943566-0.02759474564060.6719561602720.07677553494580.0866406226053-0.076390619702-0.0998216316801-0.054968630599525.0167485027-11.5693480763-29.8805056852
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 13 )AA-1 - 131 - 15
22chain 'A' and (resid 14 through 37 )AA14 - 3716 - 39
33chain 'A' and (resid 38 through 54 )AA38 - 5440 - 56
44chain 'A' and (resid 55 through 117 )AA55 - 11757 - 119
55chain 'A' and (resid 118 through 140 )AA118 - 140120 - 135
66chain 'A' and (resid 141 through 200 )AA141 - 200136 - 195
77chain 'A' and (resid 201 through 226 )AA201 - 226196 - 221
88chain 'A' and (resid 227 through 248 )AA227 - 248222 - 243
99chain 'A' and (resid 249 through 263 )AA249 - 263244 - 258
1010chain 'B' and (resid 0 through 13 )BB0 - 131 - 14
1111chain 'B' and (resid 14 through 37 )BB14 - 3715 - 38
1212chain 'B' and (resid 38 through 57 )BB38 - 5739 - 58
1313chain 'B' and (resid 58 through 75 )BB58 - 7559 - 76
1414chain 'B' and (resid 76 through 102 )BB76 - 10277 - 103
1515chain 'B' and (resid 103 through 140 )BB103 - 140104 - 136
1616chain 'B' and (resid 141 through 200 )BB141 - 200137 - 196
1717chain 'B' and (resid 201 through 226 )BB201 - 226197 - 222
1818chain 'B' and (resid 227 through 263 )BB227 - 263223 - 259
1919chain 'C' and (resid -1 through 23 )CC-1 - 231 - 17
2020chain 'C' and (resid 24 through 75 )CC24 - 7518 - 63
2121chain 'C' and (resid 76 through 140 )CC76 - 14064 - 121
2222chain 'C' and (resid 141 through 200 )CC141 - 200122 - 181
2323chain 'C' and (resid 201 through 225 )CC201 - 225182 - 206
2424chain 'C' and (resid 226 through 263 )CC226 - 263207 - 244

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • 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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