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- PDB-9pwk: P21A Mutant of E. coli Dihydrofolate Reductase Complexed with Fol... -

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Basic information

Entry
Database: PDB / ID: 9pwk
TitleP21A Mutant of E. coli Dihydrofolate Reductase Complexed with Folate and Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / P21A / DHFR
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid binding / folic acid biosynthetic process / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid binding / folic acid biosynthetic process / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / NADPH binding / 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
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsFried, S.D.E. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1915727 United States
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 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 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)19,2184
Polymers17,9931
Non-polymers1,2253
Water2,990166
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)34.063, 55.121, 81.425
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrofolate reductase


Mass: 17993.305 Da / Num. of mol.: 1 / Mutation: P21A
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-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / 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: 1.51→34.06 Å / Num. obs: 24773 / % possible obs: 99.6 % / Redundancy: 12.8 % / CC1/2: 0.969 / Rmerge(I) obs: 0.449 / Rpim(I) all: 0.131 / Rrim(I) all: 0.469 / Χ2: 0.87 / Net I/σ(I): 8.4 / Num. measured all: 316915
Reflection shellResolution: 1.51→1.53 Å / % possible obs: 97.7 % / Redundancy: 11.9 % / Rmerge(I) obs: 7.405 / Num. measured all: 14301 / Num. unique obs: 1199 / CC1/2: 0.725 / Rpim(I) all: 2.149 / Rrim(I) all: 7.718 / Χ2: 1.19 / Net I/σ(I) obs: 1.9

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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: 1.51→32.75 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2197 1215 4.98 %
Rwork0.196 --
obs0.1972 24378 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→32.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 1 166 1513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041392
X-RAY DIFFRACTIONf_angle_d0.9221905
X-RAY DIFFRACTIONf_dihedral_angle_d22.721513
X-RAY DIFFRACTIONf_chiral_restr0.056199
X-RAY DIFFRACTIONf_plane_restr0.005242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.570.32041300.31582480X-RAY DIFFRACTION96
1.57-1.640.25211350.22312564X-RAY DIFFRACTION100
1.64-1.730.23461350.2162577X-RAY DIFFRACTION100
1.73-1.840.26331360.21542574X-RAY DIFFRACTION100
1.84-1.980.24961280.22082463X-RAY DIFFRACTION95
1.98-2.180.22631320.19952510X-RAY DIFFRACTION96
2.18-2.490.24071330.19832579X-RAY DIFFRACTION98
2.49-3.140.19721390.19342648X-RAY DIFFRACTION99
3.14-32.750.18691470.1632768X-RAY DIFFRACTION100

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