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- PDB-7tq1: Crystal structure of adaptive laboratory evolved sulfonamide-resi... -

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Basic information

Entry
Database: PDB / ID: 7tq1
TitleCrystal structure of adaptive laboratory evolved sulfonamide-resistant Dihydropteroate Synthase (DHPS) from Escherichia coli in complex with 6-hydroxymethylpterin
ComponentsDihydropteroate synthase
KeywordsTRANSFERASE / DHPS / DIHYDROPTEROATE SYNTHASE / FOLP / TIM BARREL / ALPHA BETA PROTEIN / SULFONAMIDES / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / IDP98884
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to xenobiotic stimulus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like
Similarity search - Domain/homology
6-HYDROXYMETHYLPTERIN / Dihydropteroate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsStogios, P.J. / Skarina, T. / Tan, K. / Venkatesan, M. / Fruci, M. / Joachimiak, A. / Savchenko, 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
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Structure summary / Category: pdbx_database_related / struct_keywords / Item: _struct_keywords.text
Revision 1.2Jul 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 1.3Oct 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: Dihydropteroate synthase
B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2134
Polymers61,8272
Non-polymers3862
Water93752
1
A: Dihydropteroate synthase
hetero molecules

A: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2134
Polymers61,8272
Non-polymers3862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3560 Å2
ΔGint-18 kcal/mol
Surface area22640 Å2
MethodPISA
2
B: Dihydropteroate synthase
hetero molecules

B: Dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2134
Polymers61,8272
Non-polymers3862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3590 Å2
ΔGint-17 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.884, 84.571, 175.486
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


Mass: 30913.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: folP, dhpS, b3177, JW3144 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: P0AC13, dihydropteroate synthase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (w/v) PEG 3350, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 2 mM 6-hydroxymethyl- 7,8-dihydropterin diphosphate + 2mM para-aminobenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 14996 / % possible obs: 95.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.69 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.081 / Net I/σ(I): 10.05
Reflection shellResolution: 2.75→2.8 Å / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 629 / CC1/2: 0.764 / Rpim(I) all: 0.764 / % possible all: 82.2

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ajz

1ajz


Resolution: 2.73→46.77 Å / SU ML: 0.4262 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 732 4.95 %RANDOM
Rwork0.2331 14057 --
obs0.2357 14789 93.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.89 Å2
Refinement stepCycle: LAST / Resolution: 2.73→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 28 52 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374220
X-RAY DIFFRACTIONf_angle_d0.64565702
X-RAY DIFFRACTIONf_chiral_restr0.0444655
X-RAY DIFFRACTIONf_plane_restr0.0049739
X-RAY DIFFRACTIONf_dihedral_angle_d20.19611548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.940.42371190.33062305X-RAY DIFFRACTION78.12
2.94-3.240.37381510.30632711X-RAY DIFFRACTION91.67
3.24-3.70.30311450.26332951X-RAY DIFFRACTION98.54
3.7-4.670.2791510.21812984X-RAY DIFFRACTION99.49
4.67-46.770.24051660.1933106X-RAY DIFFRACTION99.15
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)
19.507128265146.091139609991.822507158554.005587566991.978850644928.79018088551-0.5158990946530.2731645417471.46026480871-0.4759542951320.4068393183190.110194879256-1.03916205183-0.1966670890440.2085142713920.5382576873820.0365853757783-0.02034027134390.3680328665380.05994152514960.65781908459510.934634407820.652744550822.681742038
27.087633459786.085721797821.779398115598.63775226404-1.750078069743.63756852036-0.9428370936381.30434669709-0.771240639866-0.7814336901370.758479738036-1.13738051455-0.3155370774890.1941199508070.5084120891741.58020240918-0.1784562146490.01731433465760.2365989286930.1054456839760.48451092483215.720729828714.04795743321.95647674527
36.482774471872.90470360695-1.697247106192.13125218613-1.299846485891.87972228864-0.3160234434480.512905617776-0.285549482511-0.3782426383060.02927877965170.0649951981701-0.6255924152560.4166517496090.2895332302020.942540821124-0.3116262024160.1804394171290.5659785260740.1288951549420.51752920036624.98190235113.14927977486.36929596026
45.62786742352-0.490031642428-0.1273368930322.17304086489-1.664442012116.07356778341-0.022396306758-0.3625452593550.0711075673479-0.191573554853-0.239667122579-0.619205784755-0.2412642771570.8072352645170.2495214460060.59701405726-0.183298358349-0.1181272926980.4357695833480.1083403432570.50295701474326.269141917110.673976778717.9811543654
57.047051191882.034620296973.263198508645.74062420639-0.5414717581844.539923616320.1477966772860.0484965109154-0.57545795594-0.0793381784419-0.0156200105084-0.6285316662810.1673777366510.160398022147-0.1716055674850.687781773661-0.0105064923385-0.01298389824410.2953846280160.05001245002550.4151250494115.20435468071.7398160665821.9941451421
67.592941197492.06964233281-1.070391777676.255215711781.259329677160.7239350769271.0918049502-1.026919891280.3890876065981.25732070942-0.742070337067-0.10136669774-0.00507166771629-0.254995947144-0.126572686020.202394765783-0.1836874279310.1206516489880.501418179035-0.1801408956640.545282930553-0.9616931304678.2048537454921.2436202968
79.826431225968.448215742670.6071086815369.55101874189-2.551711036494.090920006430.668991349914-1.093061692261.549345609190.873043174246-0.8762688582051.12331293961-0.5638028606330.2799806570310.217420048351.261023095770.05075108373790.08163981204650.563752690302-0.09203225831440.58115752518910.9574431912-21.553580014433.5417786847
83.43139599351.094344863253.008085821032.90274519117-2.863597385428.50562914920.2186191217851.08661678141-0.280876603403-0.928353894394-0.127456334867-0.4081009226290.9615031877660.167787877089-0.07455497074090.7299122728350.1965991101060.05335015501430.4992060428650.184529721390.62128891470816.3703628695-28.518919255812.7867330052
94.35490325874-1.50390933092.617994661744.56209822121-2.448078313676.102102131330.09873776225590.03512665823030.155596016777-0.223826730196-0.200692468783-1.025968190310.05172071476210.8632492312060.2147785527230.6120053803960.0640829688124-0.02517318128660.453830980520.01237599056620.59813365105625.4443412194-30.619201278928.0662329914
103.908867854643.611878634441.140261865666.632201013350.9256588874223.00468898751-0.2364253437550.05012755273920.146719810964-0.971210504538-0.0362672246375-0.453388673-0.1818256509740.2384653542910.2926875797910.8394916896020.100884163739-0.1069678754060.3906519858560.1200732744350.47419299880416.8681588077-40.312226893936.3252769791
117.667645075291.267566807640.09612317351143.14082791096-0.1806346547943.26976868297-0.0456400837037-0.03400611269010.1379335472430.546560220157-0.29331435039-0.141686942187-0.423499494815-0.234002799960.3725716692660.8609571775540.0612581159632-0.04369077616270.2800285098920.02652606926980.3339366290835.65806605509-39.067491150427.977979555
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 15 )AA0 - 151 - 16
22chain 'A' and (resid 16 through 50 )AA16 - 5017 - 44
33chain 'A' and (resid 51 through 88 )AA51 - 8845 - 82
44chain 'A' and (resid 89 through 156 )AA89 - 15683 - 146
55chain 'A' and (resid 157 through 260 )AA157 - 260147 - 250
66chain 'A' and (resid 261 through 284 )AA261 - 284251 - 274
77chain 'B' and (resid 0 through 15 )BC0 - 151 - 16
88chain 'B' and (resid 16 through 50 )BC16 - 5017 - 45
99chain 'B' and (resid 51 through 174 )BC51 - 17446 - 157
1010chain 'B' and (resid 175 through 212 )BC175 - 212158 - 195
1111chain 'B' and (resid 213 through 284 )BC213 - 284196 - 267

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