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- PDB-8scd: Crystal structure of sulfonamide resistance enzyme Sul3 in comple... -

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Basic information

Entry
Database: PDB / ID: 8scd
TitleCrystal structure of sulfonamide resistance enzyme Sul3 in complex with reaction intermediate
ComponentsSulfonamide resistance enzyme Sul3
KeywordsTRANSFERASE / TIM BARREL / ALPHA BETA PROTEIN / ANTIBIOTIC RESISTANCE / SULFONAMIDES / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSBID / CENTER FOR STRUCTURAL BIOLOGY OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Function / homology4-AMINOBENZOIC ACID / PYROPHOSPHATE 2- / Chem-XHP
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsStogios, P.J. / 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)75N93022C00035 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
DepositionApr 5, 2023Deposition 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 / pdbx_database_related
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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfonamide resistance enzyme Sul3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,75112
Polymers28,8751
Non-polymers87611
Water7,638424
1
A: Sulfonamide resistance enzyme Sul3
hetero molecules

A: Sulfonamide resistance enzyme Sul3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,50324
Polymers57,7512
Non-polymers1,75222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area5860 Å2
ΔGint-128 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.831, 123.831, 72.797
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-805-

HOH

21A-806-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfonamide resistance enzyme Sul3


Mass: 28875.369 Da / Num. of mol.: 1 / Mutation: E142A, E143A
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)

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Non-polymers , 7 types, 435 molecules

#2: Chemical ChemComp-XHP / 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one


Mass: 177.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PAB / 4-AMINOBENZOIC ACID


Mass: 137.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 5.58 Å3/Da / Density % sol: 77.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M AMMONIUM SULFATE, 5% ISOPROPANOL, 1.7 MM 6-HYDROXYMETHYL-7,8-DIHYDROPTEROATE PYROPHOSPHATE, 10 MM PABA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 39930 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 24.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.032 / Net I/σ(I): 20.58
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 16.9 % / Rmerge(I) obs: 3.178 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 1987 / CC1/2: 0.504 / Rpim(I) all: 0.795 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→47.16 Å / SU ML: 0.1798 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8627
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 3177 5.01 %RANDOM
Rwork0.1636 60210 --
obs0.1648 36295 82.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.06 Å2
Refinement stepCycle: LAST / Resolution: 2.06→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 50 424 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212122
X-RAY DIFFRACTIONf_angle_d0.49132864
X-RAY DIFFRACTIONf_chiral_restr0.0431328
X-RAY DIFFRACTIONf_plane_restr0.005362
X-RAY DIFFRACTIONf_dihedral_angle_d16.5927805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.2858130.3479263X-RAY DIFFRACTION8.29
2.09-2.120.2698280.2849539X-RAY DIFFRACTION16.79
2.12-2.160.312540.2693992X-RAY DIFFRACTION31.4
2.16-2.20.2147780.25631416X-RAY DIFFRACTION44.27
2.2-2.240.2936940.23971763X-RAY DIFFRACTION55.27
2.24-2.280.23521040.2232090X-RAY DIFFRACTION64.68
2.28-2.320.22361290.2082483X-RAY DIFFRACTION78.79
2.33-2.380.23851610.20982889X-RAY DIFFRACTION91.51
2.38-2.430.26521660.20753169X-RAY DIFFRACTION98.49
2.43-2.490.19421580.19023179X-RAY DIFFRACTION99.88
2.49-2.560.22791710.2063176X-RAY DIFFRACTION99.91
2.56-2.630.23081700.19083189X-RAY DIFFRACTION100
2.63-2.720.1851700.1843189X-RAY DIFFRACTION99.91
2.72-2.820.21971740.17423187X-RAY DIFFRACTION99.94
2.82-2.930.17971660.17173183X-RAY DIFFRACTION99.97
2.93-3.060.19591730.16473183X-RAY DIFFRACTION99.94
3.06-3.220.1821690.16433175X-RAY DIFFRACTION99.88
3.22-3.430.18911660.15493209X-RAY DIFFRACTION99.91
3.43-3.690.15761690.12783193X-RAY DIFFRACTION99.97
3.69-4.060.151700.11833172X-RAY DIFFRACTION100
4.06-4.650.15011740.12533181X-RAY DIFFRACTION99.94
4.65-5.850.1711580.143190X-RAY DIFFRACTION99.94
5.86-47.160.1781620.16993200X-RAY DIFFRACTION99.76
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)
15.55902155352-1.03921141147-0.8857073313863.5023490948-0.3656247428068.10773446437-0.0298157931539-0.1517018708680.9938621441760.0526255464072-0.06195652274510.528563273317-0.682165374461-0.6800179302530.03381827235650.160942996493-0.0154692256969-0.02900494083980.329420618698-0.1164803890060.44425676714633.0177851054-31.97979572435.6447518883
25.469313665590.271662742643-0.2648544520232.96949863547-0.2061417703233.890817897-0.227566564257-0.2661477332771.072831029940.0270479770033-0.2142958534220.38378102802-0.407413055398-0.6275640136650.02100859256660.207511242620.01713594498320.001491952133020.391526629786-0.1920551040740.4275951587832.7401752018-30.38901915338.8707069586
32.65062922550.0327903071066-0.8540683465922.906240313070.3102352749571.86888149916-0.0134536765433-0.8932565774340.5433316020280.627217776365-0.203772246620.0686742003033-0.0153577286255-0.3247256475980.1157565233450.294637885571-0.0419838788912-0.02568232088570.390835707938-0.139180419710.22948531397143.8511260385-32.225761632247.0225077666
43.367058785890.833540879034-0.5066471258913.719011610530.4691441917149.02000525378-0.1524297869240.2930597411520.1180931410380.0310296763112-0.00969746877061-0.5432092589410.1096687661490.4712284275240.195088010970.1003026476270.02068237622790.009827809370650.1681989068150.008673262702690.26912067227354.7898194018-40.969774173431.034590437
54.334571604770.5405824108560.8341995140583.201845604220.3930049146824.50054251945-0.165605747120.205047299451-0.0273579005690.0198917638878-0.0164862786149-0.1378949514470.150852220467-0.140772460380.1217206271190.106012475902-0.03513970628050.04574559444230.124626478356-0.01146962477040.12144211098943.7115261393-43.348799746529.3628836364
64.57079774308-0.9737919181531.240075280811.318558811640.5593330691072.07994630514-0.06278109923680.0902898538352-0.2132073228560.18231772915-0.1242056855950.1967710624540.373487037759-0.1832627581130.1405182800970.175068592198-0.1230317088630.06240109853690.226998661749-0.02256736934530.17183766493134.07704077-46.237311634429.932455729
79.556686292736.864291730256.211293399785.170845198565.549650990088.947422025760.36928553558-0.483432441567-0.1906494638550.7283006303910.1014034508780.036338453410.732437271644-0.0251143246262-0.3962679399230.166212895025-0.08722384972440.02974139467390.377464800215-0.001775985449930.1285009707524.7556742391-49.943361825532.4330191246
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 23 )0 - 231 - 24
22chain 'A' and (resid 24 through 57 )24 - 5725 - 58
33chain 'A' and (resid 58 through 125 )58 - 12559 - 126
44chain 'A' and (resid 126 through 161 )126 - 161127 - 162
55chain 'A' and (resid 162 through 225 )162 - 225163 - 226
66chain 'A' and (resid 226 through 248 )226 - 248227 - 249
77chain 'A' and (resid 249 through 263 )249 - 263250 - 264

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