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- PDB-9zhm: M20E Mutant of E. coli Dihydrofolate Reductase Complexed with Nic... -

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Basic information

Entry
Database: PDB / ID: 9zhm
TitleM20E Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / M20E / folate / DHFR / NADP+
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / 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: 1.07 Å
AuthorsFried, S.D.E. / 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. / Mathews, I.I. / Boxer, S.G.
History
DepositionDec 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 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)19,3676
Polymers18,0171
Non-polymers1,3505
Water4,396244
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)34.129, 44.839, 98.504
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: 18017.258 Da / Num. of mol.: 1 / Mutation: M20E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, tmrA, b0048, JW0047 / 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 6000, Manganese Chloride, imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.07→49.25 Å / Num. obs: 57527 / % possible obs: 84.6 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Χ2: 0.78 / Net I/σ(I): 13.9 / Num. measured all: 554086
Reflection shellResolution: 1.07→1.12 Å / % possible obs: 28.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.571 / Num. measured all: 9828 / Num. unique obs: 2691 / CC1/2: 0.796 / Rpim(I) all: 0.335 / Rrim(I) all: 0.665 / Χ2: 0.42 / 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: 1.07→28.05 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.158 2871 5 %
Rwork0.135 --
obs0.136 57435 84.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 83 244 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121401
X-RAY DIFFRACTIONf_angle_d1.471920
X-RAY DIFFRACTIONf_dihedral_angle_d22.985520
X-RAY DIFFRACTIONf_chiral_restr0.113200
X-RAY DIFFRACTIONf_plane_restr0.013245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.080.2939160.2635299X-RAY DIFFRACTION10
1.08-1.10.2269440.1904834X-RAY DIFFRACTION27
1.1-1.120.2472680.15441301X-RAY DIFFRACTION43
1.12-1.150.1719900.13281720X-RAY DIFFRACTION56
1.15-1.170.15021070.13022030X-RAY DIFFRACTION67
1.17-1.190.14981260.11862399X-RAY DIFFRACTION79
1.19-1.220.15251450.12022742X-RAY DIFFRACTION90
1.22-1.250.15611560.12022975X-RAY DIFFRACTION97
1.25-1.290.16591580.122995X-RAY DIFFRACTION99
1.29-1.320.17311610.11453050X-RAY DIFFRACTION100
1.32-1.370.12971610.11333070X-RAY DIFFRACTION100
1.37-1.420.14391600.11413044X-RAY DIFFRACTION100
1.42-1.470.13971620.11233061X-RAY DIFFRACTION100
1.47-1.540.13831610.1163073X-RAY DIFFRACTION100
1.54-1.620.15421630.12133092X-RAY DIFFRACTION100
1.62-1.720.16991620.13423068X-RAY DIFFRACTION100
1.72-1.850.14881620.13563089X-RAY DIFFRACTION100
1.85-2.040.14571640.1323110X-RAY DIFFRACTION100
2.04-2.340.16141640.13923129X-RAY DIFFRACTION100
2.34-2.940.18661670.15563156X-RAY DIFFRACTION100
2.94-28.050.15071740.14243327X-RAY DIFFRACTION100

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