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- PDB-9svm: Structure of dihydrofolate reductase from Burkholderia thailanden... -

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Basic information

Entry
Database: PDB / ID: 9svm
TitleStructure of dihydrofolate reductase from Burkholderia thailandensis complexed with trimethoprim and dihydrofolate
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / thymine synthesis tetrahydrofolate
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / one-carbon metabolic process / tetrahydrofolate biosynthetic process / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-NDP / TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMechulam, Y. / Schmitt, E. / Lazennec-Schurdevin, C.
Funding support France, 1items
OrganizationGrant numberCountry
Other government2020 65 00 57 France
CitationJournal: Acs Infect Dis. / Year: 2026
Title: Evolutionary Convergence on a Dihydrofolate Reductase Mutation Drives Trimethoprim-Sulfamethoxazole Resistance in Burkholderia thailandensis.
Authors: Guillier, S. / Lazennec-Schurdevin, C. / Mondange, L. / Sarilar, V. / Marchandeau, M. / Lemoigne, C. / Lamer, O. / Lescat, M. / Schmitt, E. / Mechulam, Y. / Garrec, J. / Biot, F.
History
DepositionOct 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9107
Polymers18,4901
Non-polymers1,4206
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.670, 80.340, 60.080
Angle α, β, γ (deg.)90.000, 104.980, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-388-

HOH

31A-417-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 18489.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GSM added at the N-terminus due to removal of His-Tag sequence
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Gene: C7S16_1590 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAW9D207, dihydrofolate reductase
#2: Chemical ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 800; 0.2 M Ammunium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.84→36.7 Å / Num. obs: 16730 / % possible obs: 97.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 30.47 Å2 / CC1/2: 0.996 / Net I/σ(I): 10.09
Reflection shellResolution: 1.84→1.96 Å / Num. unique obs: 2582 / CC1/2: 0.802 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→36.67 Å / SU ML: 0.2926 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 833 5.01 %
Rwork0.2092 15807 -
obs0.2104 16640 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.34 Å2
Refinement stepCycle: LAST / Resolution: 1.84→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 89 130 1489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441387
X-RAY DIFFRACTIONf_angle_d0.96511892
X-RAY DIFFRACTIONf_chiral_restr0.0451199
X-RAY DIFFRACTIONf_plane_restr0.0047277
X-RAY DIFFRACTIONf_dihedral_angle_d23.8538240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.960.36471330.35842550X-RAY DIFFRACTION95.11
1.96-2.110.33541370.2962585X-RAY DIFFRACTION97.04
2.11-2.320.25271380.23562615X-RAY DIFFRACTION97.73
2.32-2.650.25931410.21592665X-RAY DIFFRACTION98.46
2.65-3.340.23551400.20572670X-RAY DIFFRACTION99.33
3.34-36.670.18631440.17272722X-RAY DIFFRACTION99.65
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)
10.3976332925390.0184469068382-0.4119598574570.2234449158520.06048328938290.449611805492-0.0576026863837-0.016934674923-0.0191015581208-0.0860497435116-0.03288942118010.01464487090170.111017688420.05545767331799.68768728246E-60.2348510499060.00312752892673-0.007134794673030.2166174145720.003650958368680.2220429455470.490622083335-0.027642381461915.4501560132
20.163021605752-0.135264262748-0.1506244868430.1054315143280.1063529457020.1990462659860.07244998097480.05745411671020.02948834202740.00790944023501-0.01322479608780.04909744104850.000627173528351-0.3078156556331.76965791034E-50.264553013380.00872606933587-0.02272624911250.3186321268960.02799811346970.303449268393-10.537111541610.540971488319.2789654065
30.4408086392950.275422537655-0.2583238691690.191229127402-0.2446429550070.499287312891-0.0471519760260.0329993132180.0848983082747-0.0613942371845-0.0513058338516-0.0575343920440.06700226354750.189980242081-8.25562339903E-50.2697394271840.01619694277680.01699906709770.3010734824930.01579236868990.2801165304588.749475347642.8513902317411.5905596524
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 1 through 52 )1 - 521 - 52
22chain 'A' and (resid 53 through 91 )53 - 9153 - 91
33chain 'A' and (resid 92 through 164 )92 - 16492 - 164

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