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- PDB-7xi7: Human dihydrofolate reductase complexed with P39 -

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Basic information

Entry
Database: PDB / ID: 7xi7
TitleHuman dihydrofolate reductase complexed with P39
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / human DHFR / dihydrofolate reductase / P39
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
6-hexyl-5-phenyl-pyrimidine-2,4-diamine / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsVanichtanankul, J. / Saeyang, T. / Kamchonwongpaisan, S. / Yuvaniyama, J. / Yuthavong, Y.
Funding support Thailand, 1items
OrganizationGrant numberCountry
National Center for Genetic Engineering and Biotechnology (Thailand) Thailand
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural Insight into Effective Inhibitors' Binding to Toxoplasma gondii Dihydrofolate Reductase Thymidylate Synthase.
Authors: Vanichtanankul, J. / Yoomuang, A. / Taweechai, S. / Saeyang, T. / Pengon, J. / Yuvaniyama, J. / Tarnchompoo, B. / Yuthavong, Y. / Kamchonwongpaisan, S.
History
DepositionApr 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,0395
Polymers21,4811
Non-polymers5594
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.100, 83.100, 78.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3

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Components

#1: Protein Dihydrofolate reductase


Mass: 21480.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-4RI / 6-hexyl-5-phenyl-pyrimidine-2,4-diamine


Mass: 270.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.85 M ammonium sulphate, 100 mM potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLRI / Beamline: BL7.2W / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→26.56 Å / Num. obs: 47806 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.8
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 1202 / CC1/2: 0.763

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DDR

4ddr


Resolution: 1.65→22.18 Å / SU ML: 0.1647 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 19.4324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1936 2390 5 %
Rwork0.1657 45416 -
obs0.1671 47806 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 1.65→22.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 35 293 1830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611570
X-RAY DIFFRACTIONf_angle_d0.89562120
X-RAY DIFFRACTIONf_chiral_restr0.0585222
X-RAY DIFFRACTIONf_plane_restr0.0081271
X-RAY DIFFRACTIONf_dihedral_angle_d11.9623603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.29641400.24692634X-RAY DIFFRACTION96.72
1.68-1.720.23491370.22482635X-RAY DIFFRACTION96.59
1.72-1.760.23941370.21722675X-RAY DIFFRACTION97.1
1.76-1.80.26571400.20722641X-RAY DIFFRACTION97.03
1.8-1.850.29421360.19452656X-RAY DIFFRACTION97.28
1.85-1.910.22381430.18272642X-RAY DIFFRACTION97.51
1.91-1.970.20091400.17162634X-RAY DIFFRACTION97.54
1.97-2.040.18121400.15792645X-RAY DIFFRACTION97.79
2.04-2.120.21511410.16372701X-RAY DIFFRACTION97.93
2.12-2.220.19261410.16122675X-RAY DIFFRACTION98.12
2.22-2.330.20611430.16062661X-RAY DIFFRACTION98.32
2.33-2.480.20241430.16042728X-RAY DIFFRACTION98.52
2.48-2.670.18561350.16932636X-RAY DIFFRACTION98.68
2.67-2.940.20181450.17422722X-RAY DIFFRACTION98.93
2.94-3.360.20041440.15322708X-RAY DIFFRACTION99.23
3.37-4.230.12881420.13312719X-RAY DIFFRACTION99.41
4.23-22.180.16661430.1562704X-RAY DIFFRACTION99.41

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