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- PDB-9pwm: Dihydrofolate Reductase Complexed with Folate and Nicotinamide Ad... -

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Basic information

Entry
Database: PDB / ID: 9pwm
TitleDihydrofolate Reductase Complexed with Folate and Nicotinamide Adenine Dinucleotide Phosphate (Oxidized Form)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / wild-type / 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: 0.89 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 1.0Jan 21, 2026Provider: repository / Type: Initial release

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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)19,63710
Polymers18,0671
Non-polymers1,5699
Water4,936274
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)33.880, 44.860, 98.550
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: 18067.338 Da / Num. of mol.: 1
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-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.27 %
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: BL12-1 / 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: 0.89→33.88 Å / Num. obs: 115332 / % possible obs: 99.6 % / Redundancy: 18.56 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Net I/σ(I): 23.96
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
0.89-0.911.96181190.5442.0371
0.91-0.941.18182310.8031.2181
0.94-0.970.78180300.9270.8021
0.97-10.55478180.960.5691
1-1.030.38175640.980.3921
1.03-1.060.26273390.990.271
1.06-1.10.18870550.9940.1931
1.1-1.150.14168530.9970.1451
1.15-1.20.11665350.9980.1191
1.2-1.260.10662900.9980.1091
1.26-1.330.09659490.9980.0981
1.33-1.410.08457140.9980.0871
1.41-1.50.07453010.9980.0761
1.5-1.620.06549910.9990.0671
1.62-1.780.0646080.9990.0611
1.78-1.990.05541820.9990.0561
1.99-2.30.05336960.9990.0541
2.3-2.810.0531130.9990.0521
2.81-3.980.04824880.9990.0491
3.98-33.880.04814560.9990.0491

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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: 0.89→27.92 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.156 5766 5 %
Rwork0.1456 --
obs0.1461 115324 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.89→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 7 274 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071451
X-RAY DIFFRACTIONf_angle_d1.3191987
X-RAY DIFFRACTIONf_dihedral_angle_d18.869537
X-RAY DIFFRACTIONf_chiral_restr0.1203
X-RAY DIFFRACTIONf_plane_restr0.009250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.89-0.90.38781710.3673254X-RAY DIFFRACTION90
0.9-0.910.32321900.31083587X-RAY DIFFRACTION99
0.91-0.920.25571920.26133657X-RAY DIFFRACTION100
0.92-0.930.23851890.20653598X-RAY DIFFRACTION100
0.93-0.950.19781910.17873630X-RAY DIFFRACTION100
0.95-0.960.17241910.16473632X-RAY DIFFRACTION100
0.96-0.970.19291910.15673617X-RAY DIFFRACTION100
0.97-0.990.16641900.14693611X-RAY DIFFRACTION100
0.99-10.17851930.1443676X-RAY DIFFRACTION100
1-1.020.14741900.13433617X-RAY DIFFRACTION100
1.02-1.040.14381910.13253606X-RAY DIFFRACTION100
1.04-1.060.13261910.13163649X-RAY DIFFRACTION100
1.06-1.080.13981920.12043642X-RAY DIFFRACTION100
1.08-1.10.11811920.11753657X-RAY DIFFRACTION100
1.1-1.120.11741920.11073645X-RAY DIFFRACTION100
1.12-1.150.12241920.1043648X-RAY DIFFRACTION100
1.15-1.180.12171910.10153639X-RAY DIFFRACTION100
1.18-1.210.12281920.10353649X-RAY DIFFRACTION100
1.21-1.240.11561930.11093663X-RAY DIFFRACTION100
1.24-1.280.13071920.11463650X-RAY DIFFRACTION100
1.28-1.330.13231930.11483657X-RAY DIFFRACTION100
1.33-1.380.13661920.12043662X-RAY DIFFRACTION100
1.38-1.450.12861960.12593709X-RAY DIFFRACTION100
1.45-1.520.14871930.12083675X-RAY DIFFRACTION100
1.52-1.620.13071950.12783707X-RAY DIFFRACTION100
1.62-1.740.15571930.13443682X-RAY DIFFRACTION100
1.74-1.920.14651970.13983716X-RAY DIFFRACTION100
1.92-2.190.16211960.1463747X-RAY DIFFRACTION100
2.19-2.760.17261970.16833728X-RAY DIFFRACTION98
2.76-27.920.17732080.17433948X-RAY DIFFRACTION99

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