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- PDB-7myl: Crystal structure of DfrA1 dihydrofolate reductase in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7myl
TitleCrystal structure of DfrA1 dihydrofolate reductase in complex with TRIMETHOPRIM
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Trimetoprim resistant dihydrofolate reductase / DfrA1
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
TRIMETHOPRIM / dihydrofolate reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsErlandsen, H. / Wright, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1 R01AI111957 United States
CitationJournal: Commun Biol / Year: 2022
Title: Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens.
Authors: Krucinska, J. / Lombardo, M.N. / Erlandsen, H. / Estrada, A. / Si, D. / Viswanathan, K. / Wright, D.L.
History
DepositionMay 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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: Dihydrofolate reductase
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
F: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,40512
Polymers108,6646
Non-polymers1,7426
Water88349
1
A: Dihydrofolate reductase
hetero molecules

D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8024
Polymers36,2212
Non-polymers5812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3420 Å2
ΔGint-15 kcal/mol
Surface area14840 Å2
MethodPISA
2
B: Dihydrofolate reductase
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8024
Polymers36,2212
Non-polymers5812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-18 kcal/mol
Surface area15110 Å2
MethodPISA
3
E: Dihydrofolate reductase
F: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8024
Polymers36,2212
Non-polymers5812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-13 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.072, 72.890, 125.122
Angle α, β, γ (deg.)90.000, 90.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dihydrofolate reductase


Mass: 18110.588 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: dfrA1, AM447_11900, EXT45_00270 / Production host: Escherichia coli (E. coli) / References: UniProt: A4GRC7, dihydrofolate reductase
#2: Chemical
ChemComp-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H18N4O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.33 Å3/Da / Density % sol: 47.11 % / Description: hexagonal crystals
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG3350, 0.1M Na-Cacodylate pH 6.5, 0.36M MgCl2 and 2 mM DTT
PH range: 6.1-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2020
RadiationMonochromator: Double Crystal Monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.15→72.89 Å / Num. obs: 53224 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.078 / Rrim(I) all: 0.206 / Net I/σ(I): 7.6
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4327 / CC1/2: 0.558 / Rpim(I) all: 0.379 / Rrim(I) all: 0.983 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ECC

5ecc


Resolution: 2.15→63.06 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.427 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 2718 5.1 %RANDOM
Rwork0.2147 ---
obs0.2173 50486 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.6 Å2 / Biso mean: 29.331 Å2 / Biso min: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.63 Å2
2--2.38 Å20 Å2
3----1.76 Å2
Refinement stepCycle: final / Resolution: 2.15→63.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 126 49 7617
Biso mean--26.73 16.63 -
Num. residues----940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177390
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.63310519
X-RAY DIFFRACTIONr_angle_other_deg1.151.57817011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1535933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53824.011354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.029151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2771524
X-RAY DIFFRACTIONr_chiral_restr0.0590.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021757
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 165 -
Rwork0.309 3755 -
all-3920 -
obs--97.59 %

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