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- PDB-7fpo: DHFR:NADP+:FOL complex at 280 K (crystal 4) -

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Basic information

Entry
Database: PDB / ID: 7fpo
TitleDHFR:NADP+:FOL complex at 280 K (crystal 4)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Dihydrofolate Reductase
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.06 Å
AuthorsGreisman, J.B. / Dalton, K.M. / Brookner, D.E. / Hekstra, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
Searle Scholars ProgramSSP-2018-3240 United States
George W. Merck Fund in the New York Community Trust338034 United States
National Institutes of Health/Office of the DirectorDP2-GM141000 United States
National Science Foundation (NSF, United States)DGE1745303 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism.
Authors: Greisman, J.B. / Dalton, K.M. / Brookner, D.E. / Klureza, M.A. / Sheehan, C.J. / Kim, I.S. / Henning, R.W. / Russi, S. / Hekstra, D.R.
History
DepositionSep 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)19,4016
Polymers18,0511
Non-polymers1,3505
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.184, 45.549, 99.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Dihydrofolate reductase


Mass: 18051.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / 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.: 165 / 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

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20 mM imadazole (pH 5.4-5.8), 16-21% PEG 400, 125 mM MnCl2
PH range: 5.4 - 5.8

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Data collection

DiffractionMean temperature: 280 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.826533 / Wavelength: 0.826533 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826533 Å / Relative weight: 1
ReflectionResolution: 1.06→45.55 Å / Num. obs: 135454 / % possible obs: 99.9 % / Redundancy: 25.7 % / Biso Wilson estimate: 15.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.521 / Rpim(I) all: 0.106 / Net I/σ(I): 18.4
Reflection shellResolution: 1.06→1.08 Å / % possible obs: 98.4 % / Redundancy: 25.4 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7295 / CC1/2: 0.336 / Rpim(I) all: 2.364

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Processing

Software
NameVersionClassification
DIALS3.5.2data reduction
DIALS3.5.2data scaling
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7LVC

7lvc


Resolution: 1.06→32.31 Å / SU ML: 0.1358 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.3993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1707 6563 4.95 %
Rwork0.1474 126036 -
obs0.1485 132599 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.07 Å2
Refinement stepCycle: LAST / Resolution: 1.06→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 83 165 1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00871700
X-RAY DIFFRACTIONf_angle_d1.1332351
X-RAY DIFFRACTIONf_chiral_restr0.0937233
X-RAY DIFFRACTIONf_plane_restr0.012313
X-RAY DIFFRACTIONf_dihedral_angle_d13.2746628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.070.37941940.36753313X-RAY DIFFRACTION77.47
1.07-1.080.35811690.3453672X-RAY DIFFRACTION84.88
1.08-1.10.33462040.33023859X-RAY DIFFRACTION90.01
1.1-1.110.31912300.32333956X-RAY DIFFRACTION92.28
1.11-1.130.33342290.30074076X-RAY DIFFRACTION96.05
1.13-1.140.27262060.2864294X-RAY DIFFRACTION98.06
1.14-1.160.26921980.27574235X-RAY DIFFRACTION99.02
1.16-1.180.3062560.27794244X-RAY DIFFRACTION99.6
1.18-1.190.30422110.2724298X-RAY DIFFRACTION99.82
1.19-1.210.29972130.26224325X-RAY DIFFRACTION99.82
1.21-1.230.25842560.23214228X-RAY DIFFRACTION99.89
1.23-1.260.22722020.21624316X-RAY DIFFRACTION99.91
1.26-1.280.22822190.20694282X-RAY DIFFRACTION99.43
1.28-1.310.22242300.17854301X-RAY DIFFRACTION99.98
1.31-1.340.18112350.16824269X-RAY DIFFRACTION99.65
1.34-1.370.2062390.16444278X-RAY DIFFRACTION99.93
1.37-1.40.19522220.16084297X-RAY DIFFRACTION99.93
1.4-1.440.18772190.1574274X-RAY DIFFRACTION99.91
1.44-1.480.17422460.13454299X-RAY DIFFRACTION99.89
1.48-1.530.15652260.11854261X-RAY DIFFRACTION99.98
1.53-1.580.15252440.10814319X-RAY DIFFRACTION99.91
1.58-1.650.13562350.09914265X-RAY DIFFRACTION100
1.65-1.720.14932140.10464313X-RAY DIFFRACTION99.91
1.72-1.810.13972000.10824315X-RAY DIFFRACTION99.73
1.81-1.930.12591970.09684297X-RAY DIFFRACTION100
1.93-2.070.12281900.10044342X-RAY DIFFRACTION99.87
2.07-2.280.12182570.11064289X-RAY DIFFRACTION99.82
2.28-2.610.14932200.12894266X-RAY DIFFRACTION99.67
2.61-3.290.19562030.15574285X-RAY DIFFRACTION99.53
3.29-32.310.16381990.15694268X-RAY DIFFRACTION98.72

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