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- PDB-7mqp: E. coli dihydrofolate reductase complexed with 4'-chloro-3'-(4-(2... -

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Basic information

Entry
Database: PDB / ID: 7mqp
TitleE. coli dihydrofolate reductase complexed with 4'-chloro-3'-(4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl)-[1,1'-biphenyl]-4-carboxamide (UCP1228)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Inhibitor / antifolate / DHFR
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / 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-ZM4 / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLombardo, M.N. / Wright, D.L.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
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 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3359
Polymers18,2631
Non-polymers1,0728
Water1,02757
1
A: Dihydrofolate reductase
hetero molecules

A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,66918
Polymers36,5252
Non-polymers2,14416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3800 Å2
ΔGint-197 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.681, 66.681, 213.752
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dihydrofolate reductase


Mass: 18262.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, folA_1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TR70, dihydrofolate reductase
#2: Chemical ChemComp-ZM4 / 3'-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-4'-methyl[1,1'-biphenyl]-4-carboxamide


Mass: 399.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.76 Å3/Da / Density % sol: 67.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.3-0.35 M lithium sulfate, 15-19% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→57.81 Å / Num. obs: 17232 / % possible obs: 99.72 % / Redundancy: 1.2 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 21.82
Reflection shellResolution: 2.102→2.177 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 3.73 / Num. unique obs: 1663 / CC1/2: 1 / CC star: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RF7

1rf7


Resolution: 2.1→57.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.225 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 803 4.7 %RANDOM
Rwork0.1903 ---
obs0.1923 16430 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 163.31 Å2 / Biso mean: 65.274 Å2 / Biso min: 42.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20.66 Å20 Å2
2--1.33 Å2-0 Å2
3----4.31 Å2
Refinement stepCycle: final / Resolution: 2.1→57.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 65 57 1406
Biso mean--91.79 68.09 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021415
X-RAY DIFFRACTIONr_bond_other_d0.0030.021234
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.9911936
X-RAY DIFFRACTIONr_angle_other_deg1.0883.0052866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1824.41268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99415222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.181159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211571
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02288
LS refinement shellResolution: 2.102→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 63 -
Rwork0.296 1174 -
all-1237 -
obs--99.92 %

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