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- PDB-6clv: Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208... -

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Basic information

Entry
Database: PDB / ID: 6clv
TitleStaphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure
ComponentsDihydropteroate synthase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance mutations / sulfonamide resistance
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to antibiotic / metal ion binding
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-6MB / Dihydropteroate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsGajewski, S. / Griffith, E.C. / Wu, Y. / White, S.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070721-08 United States
St. Jude Children's Research Hospital (ALSAC) United States
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: Front Microbiol / Year: 2018
Title: The Structural and Functional Basis for Recurring Sulfa Drug Resistance Mutations inStaphylococcus aureusDihydropteroate Synthase.
Authors: Griffith, E.C. / Wallace, M.J. / Wu, Y. / Kumar, G. / Gajewski, S. / Jackson, P. / Phelps, G.A. / Zheng, Z. / Rock, C.O. / Lee, R.E. / White, S.W.
History
DepositionMar 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropteroate synthase
B: Dihydropteroate synthase
C: Dihydropteroate synthase
D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9557
Polymers129,6284
Non-polymers1,3273
Water1,78399
1
A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8492
Polymers32,4071
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8492
Polymers32,4071
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8492
Polymers32,4071
Non-polymers4421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)32,4071
Polymers32,4071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Dihydropteroate synthase
D: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2563
Polymers64,8142
Non-polymers4421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-21 kcal/mol
Surface area19710 Å2
MethodPISA
6
B: Dihydropteroate synthase
C: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6994
Polymers64,8142
Non-polymers8852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-20 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.750, 79.750, 175.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Dihydropteroate synthase / / DHPS / Dihydropteroate pyrophosphorylase


Mass: 32406.936 Da / Num. of mol.: 4 / Mutation: F17L, E208K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folP, dpsA / Production host: Escherichia coli (E. coli) / References: UniProt: O05701, dihydropteroate synthase
#2: Chemical ChemComp-6MB / 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl]amino}-N-(3,4-dimethyl-1,2-oxazol-5-yl)benzene-1-sulfonamide


Mass: 442.452 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H18N8O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Nitrate, and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97918 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.64
ReflectionResolution: 2.3→47.432 Å / Num. obs: 201103 / % possible obs: 99.7 % / Redundancy: 4.2 % / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.3444 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.432 Å / Cross valid method: THROUGHOUT / σ(F): 52.06 / Phase error: 33.57 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2099 2546 5.25 %
Rwork0.1907 --
obs0.2119 48470 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7350 0 93 99 7542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037557
X-RAY DIFFRACTIONf_angle_d0.60410279
X-RAY DIFFRACTIONf_dihedral_angle_d10.6384534
X-RAY DIFFRACTIONf_chiral_restr0.0471241
X-RAY DIFFRACTIONf_plane_restr0.0041313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.34440.30921360.28552568X-RAY DIFFRACTION95
2.3444-2.39220.29141360.28122491X-RAY DIFFRACTION95
2.3922-2.44420.28671480.28012559X-RAY DIFFRACTION94
2.4442-2.50110.31691470.28172550X-RAY DIFFRACTION95
2.5011-2.56360.27391230.26462544X-RAY DIFFRACTION95
2.5636-2.63290.29831380.26582549X-RAY DIFFRACTION95
2.6329-2.71030.26041290.25492544X-RAY DIFFRACTION95
2.7103-2.79770.26611470.24372537X-RAY DIFFRACTION95
2.7977-2.89770.26781630.2442520X-RAY DIFFRACTION94
2.8977-3.01360.26831310.23892575X-RAY DIFFRACTION95
3.0136-3.15070.25321420.22562536X-RAY DIFFRACTION95
3.1507-3.31660.23261300.22862596X-RAY DIFFRACTION95
3.3166-3.52420.26561170.22432538X-RAY DIFFRACTION96
3.5242-3.79590.25211640.20862554X-RAY DIFFRACTION94
3.7959-4.17730.21861620.19432540X-RAY DIFFRACTION94
4.1773-4.78020.18081640.17532504X-RAY DIFFRACTION94
4.7802-6.01650.1941130.162604X-RAY DIFFRACTION96
6.0165-32.94620.21791560.1872573X-RAY DIFFRACTION94
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)
11.2985-0.0136-0.29741.70440.43260.61490.03190.11460.2814-0.1776-0.1937-0.3070.09270.4181-0.01070.3395-0.00440.00150.59450.14130.283791.7748130.61558.5791
22.3677-0.2353-0.17051.14440.47890.57680.23460.30820.27390.0985-0.1878-0.1538-0.2676-0.0260.21460.30030.038-0.02480.36660.01050.161778.7323133.378516.3874
30.259-0.1417-0.07970.5017-0.04730.95220.11250.11670.0364-0.1536-0.09760.01030.22330.150.19980.33630.0941-0.01540.4250.0220.121678.0433117.336911.5553
44.7685-0.33282.12621.1885-0.6623.49120.0675-0.2034-0.67710.13630.0295-0.00790.25490.0727-0.07880.4210.03350.07230.3260.04420.3875109.4052115.2948-19.8716
52.1374-0.7419-0.2762.4175-0.28261.089-0.0716-0.2227-0.1598-0.17480.0401-0.15290.00160.30360.13150.3244-0.01030.03420.37310.01160.1962114.2517129.9562-21.5056
61.50760.20190.36661.10690.40270.8353-0.03970.054-0.1150.00180.0376-0.0688-0.0624-0.17760.00020.3246-0.02650.05350.3216-0.01370.160796.2097128.0206-25.4132
72.94080.70930.43552.0927-0.04340.34760.0306-0.032-0.35540.0847-0.03020.1630.1756-0.2503-0.01780.3653-0.0570.06250.46540.04240.274562.6514113.3967-31.3389
81.2911-0.3836-0.0310.8692-0.02360.8424-0.01460.0918-0.0516-0.00850.04220.0578-0.0723-0.052-0.03150.3044-0.04230.02540.36790.01480.138472.729125.3738-38.547
90.20360.2374-0.02380.2521-0.0114-0.0028-0.137-0.1144-0.35-0.0778-0.0093-0.26970.06140.33610.01740.60490.28630.05650.54210.05110.435592.137184.4865-0.3575
100.4014-0.24870.01930.2073-0.18880.3905-0.1799-0.1759-0.5657-0.1121-0.2910.08310.72070.1601-0.50391.05930.52690.04060.1626-0.10290.258779.375378.9499-3.8479
110.234-0.26140.28390.354-0.29420.89040.12070.1086-0.0726-0.5576-0.11580.22050.3822-0.01070.12470.76810.1259-0.14460.4724-0.06450.399469.082689.9866-5.4083
120.62150.0577-0.16540.21650.01590.29830.12910.0445-0.0625-0.18550.06010.01550.02890.03430.46520.94920.4966-0.16780.5077-0.06630.286477.626793.3706-2.3496
132.51810.79141.06650.5081-0.21462.3275-0.01720.39730.0998-0.3405-0.0447-0.0418-0.21890.3870.08820.7150.18530.04390.46310.05880.143484.5925106.318-11.7775
140.20940.06680.34170.80370.16980.66230.0197-0.0215-0.1359-0.1255-0.110.23470.26530.1118-0.01760.57530.1475-0.06350.45110.00820.20580.6477101.32115.3025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 97 )
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 263 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 74 )
5X-RAY DIFFRACTION5chain 'B' and (resid 75 through 157 )
6X-RAY DIFFRACTION6chain 'B' and (resid 158 through 263 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 97 )
8X-RAY DIFFRACTION8chain 'C' and (resid 98 through 264 )
9X-RAY DIFFRACTION9chain 'D' and (resid 2 through 74 )
10X-RAY DIFFRACTION10chain 'D' and (resid 75 through 138 )
11X-RAY DIFFRACTION11chain 'D' and (resid 139 through 192 )
12X-RAY DIFFRACTION12chain 'D' and (resid 193 through 203 )
13X-RAY DIFFRACTION13chain 'D' and (resid 204 through 215 )
14X-RAY DIFFRACTION14chain 'D' and (resid 216 through 264 )

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