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- PDB-7s2i: Crystal structure of sulfonamide resistance enzyme Sul1 in comple... -

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Basic information

Entry
Database: PDB / ID: 7s2i
TitleCrystal structure of sulfonamide resistance enzyme Sul1 in complex with 6-hydroxymethylpterin
ComponentsSul1
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 / homologyDihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 6-HYDROXYMETHYLPTERIN
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsStogios, P.J. / Skarina, T. / Kim, Y. / 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: Sul1
B: Sul1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,83119
Polymers60,3312
Non-polymers1,50017
Water5,098283
1
A: Sul1
hetero molecules

B: Sul1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,83119
Polymers60,3312
Non-polymers1,50017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
Buried area5690 Å2
ΔGint-97 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.568, 186.568, 186.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

21A-527-

HOH

31B-551-

HOH

41B-554-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sul1


Mass: 30165.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: Sul1 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold

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Non-polymers , 5 types, 300 molecules

#2: Chemical ChemComp-HHR / 6-HYDROXYMETHYLPTERIN


Mass: 193.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M potassium sulfate, 20% w/v PEG3350, 6-hydroxymethylpterin

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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 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 48327 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 55.06 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.034 / Net I/σ(I): 24.53
Reflection shellResolution: 2.32→2.36 Å / Rmerge(I) obs: 2.135 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 2375 / CC1/2: 0.52 / Rpim(I) all: 0.619 / % possible all: 100

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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: 2.32→29.14 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1951 2000 4.14 %
Rwork0.1761 46268 -
obs0.1769 48268 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.99 Å2
Refinement stepCycle: LAST / Resolution: 2.32→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 89 283 4380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544162
X-RAY DIFFRACTIONf_angle_d0.76345643
X-RAY DIFFRACTIONf_chiral_restr0.0504639
X-RAY DIFFRACTIONf_plane_restr0.0071738
X-RAY DIFFRACTIONf_dihedral_angle_d5.9556589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.29741410.28073269X-RAY DIFFRACTION100
2.38-2.440.24611400.24413245X-RAY DIFFRACTION100
2.44-2.520.24151400.22733237X-RAY DIFFRACTION100
2.52-2.60.22261410.22163246X-RAY DIFFRACTION100
2.6-2.690.22911410.20213262X-RAY DIFFRACTION100
2.69-2.80.23331410.20693256X-RAY DIFFRACTION100
2.8-2.930.26351410.2263258X-RAY DIFFRACTION100
2.93-3.080.2521400.21293278X-RAY DIFFRACTION100
3.08-3.270.24041440.20023300X-RAY DIFFRACTION100
3.27-3.520.20631420.18773295X-RAY DIFFRACTION100
3.52-3.880.17961440.15513321X-RAY DIFFRACTION100
3.88-4.440.15991440.13733344X-RAY DIFFRACTION99.94
4.44-5.580.15521470.14873387X-RAY DIFFRACTION100
5.59-29.140.17991540.16953570X-RAY DIFFRACTION99.52
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)
13.366926302930.367097892149-0.6056457846574.716562129371.180464800491.487471951840.2360885411910.489745672410.118781700799-0.661407038161-0.112704018111-0.129606805988-0.2139346046750.119502676289-0.09945443603870.450536211980.0178960762780.1061299978580.728994843321-0.008655230464390.464275689984-3.41516285224-49.8463709108-7.59136522868
23.741115035442.19296091783-3.497153195692.76945235863-1.50233757274.807163668920.002207186571440.155010527754-0.0890900506608-0.341441877201-0.367878284444-1.099563817960.2790213720111.383068976660.7266828767510.4478624227-0.1100275609440.1850495573281.02414439206-0.05820683848150.94470886218713.2550727965-48.76825346810.827952972758
33.22800927137-0.179667985738-1.381758383852.00601166766-0.4420412736782.543918266530.200821876331-0.2769627838410.37475160671-0.0302106843250.0581772980994-0.385383048129-0.1817337923950.66017399032-0.2168566460090.328450965299-0.1458362595730.06484998280430.73955349202-0.1502977548820.5579075047683.00692021276-45.095974746211.7670992815
49.439582017146.86752007255.226424657935.284324447143.684946906813.810784779170.227502957412-0.135630405680.396188614623-0.00486247870221-0.2063337105410.311113060733-0.02275228749370.451005194661-0.1625755430820.3509135477430.10055471099-0.02214184937180.55075572734-0.1170932981230.651878046347-12.6163834325-68.90429576584.96393569033
53.414061222262.960131938551.225657410084.64362566619-0.5885773616631.923905532940.114518426228-0.2003104873110.7787603831340.2183187394950.05368216466850.321113646604-0.0668716875768-0.115723434773-0.2006216729920.3799018247310.124727145425-0.07791750864980.467047210774-0.1562991191420.636521299788-14.3631943734-72.19587358975.08637357412
62.073388526130.0616467781376-0.1343683728743.147231801771.289806986135.148533811080.1792041829010.100301402325-0.36128940446-0.00989060890390.0493881131104-0.1955423984070.3859656994320.292366094181-0.1955511031360.3604082469110.150283784202-0.0825756399470.4257539764-0.129312737410.635331806338-12.0562255803-85.30366170122.93121572878
73.72588276989-3.403106302123.04490934185.62734299496-5.280919264916.224768080870.3402851607920.748442228332-0.372062591681-1.132897317-0.5636976734810.3571289834410.4153376888890.04534532275890.3033332583770.6159549813820.173325834411-0.1632826764740.742756867579-0.3665334169670.836971825993-21.5742025385-86.3030323686-14.6191323659
81.96702494367-0.5368483531-1.07487649322.390180666670.04826474672431.731935810970.1457418443250.452349553481-0.392894736346-0.280961417468-0.1462351925880.631061295290.0272220245021-0.37775455869-0.0154450836080.3360263710180.101790442844-0.1749295697020.595448584965-0.1759121632720.70396627232-30.8653421076-73.9778180835-6.68819085862
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 108 )AA1 - 1081 - 108
22chain 'A' and (resid 109 through 141 )AA109 - 141109 - 137
33chain 'A' and (resid 142 through 268 )AA142 - 268138 - 264
44chain 'B' and (resid 1 through 23 )BB1 - 231 - 23
55chain 'B' and (resid 24 through 57 )BB24 - 5724 - 57
66chain 'B' and (resid 58 through 117 )BB58 - 11758 - 117
77chain 'B' and (resid 118 through 163 )BB118 - 163118 - 156
88chain 'B' and (resid 164 through 270 )BB164 - 270157 - 263

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