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- PDB-8ucx: Dihydrofolate Reductase Complexed with Folate -

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Basic information

Entry
Database: PDB / ID: 8ucx
TitleDihydrofolate Reductase Complexed with Folate
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / wild-type / folate / 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
FOLIC ACID / : / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsFried, S.D.E. / 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. / Mao, Y. / Boxer, S.G.
History
DepositionSep 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)18,6745
Polymers18,0671
Non-polymers6064
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.400, 104.400, 33.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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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 / Plasmid: pET22b-ecDHFR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TR70
#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-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Mixed 1 microliter of ecDHFR-FOL in 20 mM imidazole at pH 7.0 with 1 microliter of a reservoir solution containing 14%(w/v) PEG 6000, 300 mM MnCl2, and 20 mM imidazole at pH 7.0

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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: Aug 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→36.91 Å / Num. obs: 25931 / % possible obs: 99.8 % / Redundancy: 25.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.023 / Rrim(I) all: 0.118 / Χ2: 0.93 / Net I/σ(I): 17.6 / Num. measured all: 658288
Reflection shellResolution: 1.57→1.59 Å / % possible obs: 95.3 % / Redundancy: 20 % / Rmerge(I) obs: 1.743 / Num. measured all: 23924 / Num. unique obs: 1199 / CC1/2: 0.721 / Rpim(I) all: 0.385 / Rrim(I) all: 1.787 / Χ2: 0.75 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→36.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 1304 5.03 %
Rwork0.1858 --
obs0.1873 25916 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.57→36.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 3 134 1423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111420
X-RAY DIFFRACTIONf_angle_d1.2641943
X-RAY DIFFRACTIONf_dihedral_angle_d13.757530
X-RAY DIFFRACTIONf_chiral_restr0.079200
X-RAY DIFFRACTIONf_plane_restr0.011258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.630.30381430.23642674X-RAY DIFFRACTION98
1.63-1.70.2661420.20532701X-RAY DIFFRACTION100
1.71-1.790.23731450.20342730X-RAY DIFFRACTION100
1.8-1.910.1991440.18862715X-RAY DIFFRACTION100
1.91-2.050.23991400.17572728X-RAY DIFFRACTION100
2.05-2.260.22821430.18442738X-RAY DIFFRACTION100
2.26-2.590.23631460.19212734X-RAY DIFFRACTION100
2.59-3.260.20811500.20782747X-RAY DIFFRACTION100
3.26-36.910.19351510.16542845X-RAY DIFFRACTION100

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