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- PDB-9pxc: Y100F Mutant of E. coli Dihydrofolate Reductase Complexed with NA... -

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Basic information

Entry
Database: PDB / ID: 9pxc
TitleY100F Mutant of E. coli Dihydrofolate Reductase Complexed with NADP+ (oxidized form)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Y100F / DHFR
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsFried, S.D.E. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118044 United States
CitationJournal: To Be Published
Title: Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase
Authors: Fried, S.D.E. / Mukherjee, S. / Boxer, S.G.
History
DepositionAug 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: 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)18,7873
Polymers18,0031
Non-polymers7832
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.326, 57.425, 73.992
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

21A-320-

HOH

31A-324-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 18003.340 Da / Num. of mol.: 1 / Mutation: Y100F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, tmrA, b0048, JW0047 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 6000, calcium chloride, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.37→37 Å / Num. obs: 6365 / % possible obs: 99.7 % / Redundancy: 10 % / CC1/2: 0.994 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.075 / Rrim(I) all: 0.239 / Χ2: 0.97 / Net I/σ(I): 7.5 / Num. measured all: 63920
Reflection shellResolution: 2.37→2.46 Å / % possible obs: 98.4 % / Redundancy: 9.8 % / Rmerge(I) obs: 1.925 / Num. measured all: 6361 / Num. unique obs: 648 / CC1/2: 0.426 / Rpim(I) all: 0.64 / Rrim(I) all: 2.032 / Χ2: 0.96 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→37 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 318 5.01 %
Rwork0.2058 --
obs0.2087 6343 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 1 26 1304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021314
X-RAY DIFFRACTIONf_angle_d0.7331797
X-RAY DIFFRACTIONf_dihedral_angle_d16.771480
X-RAY DIFFRACTIONf_chiral_restr0.053193
X-RAY DIFFRACTIONf_plane_restr0.005227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.980.32171540.2492934X-RAY DIFFRACTION99
2.98-370.24131640.19073091X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.1543 Å / Origin y: 13.4668 Å / Origin z: -17.6522 Å
111213212223313233
T0.1705 Å20.0405 Å20.0132 Å2-0.1666 Å2-0.0336 Å2--0.2204 Å2
L2.2581 °20.4375 °2-0.6572 °2-1.7702 °2-0.1851 °2--2.7209 °2
S-0.0709 Å °0.0952 Å °-0.077 Å °-0.1969 Å °0.0561 Å °-0.0938 Å °0.1433 Å °0.0298 Å °0.0008 Å °
Refinement TLS groupSelection details: all

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