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- PDB-7fpp: DHFR:NADP+:FOL complex at 280 K (crystal 5) -

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Basic information

Entry
Database: PDB / ID: 7fpp
TitleDHFR:NADP+:FOL complex at 280 K (crystal 5)
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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / 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: 1.03 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 9, 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)34.202, 45.473, 99.093
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: 2.13 Å3/Da / Density % sol: 42.37 %
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: 1.03→32.33 Å / Num. obs: 134271 / % possible obs: 90.6 % / Redundancy: 29.4 % / Biso Wilson estimate: 14.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.018 / Net I/σ(I): 28.7
Reflection shellResolution: 1.03→1.05 Å / % possible obs: 59.8 % / Redundancy: 28.1 % / Rmerge(I) obs: 7.03 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5076 / CC1/2: 0.324 / Rpim(I) all: 1.327

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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: 1.03→21.06 Å / SU ML: 0.1253 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.6505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.149 6667 5 %
Rwork0.1251 126750 -
obs0.1262 133417 90.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.36 Å2
Refinement stepCycle: LAST / Resolution: 1.03→21.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 83 165 1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951700
X-RAY DIFFRACTIONf_angle_d1.15352351
X-RAY DIFFRACTIONf_chiral_restr0.0973233
X-RAY DIFFRACTIONf_plane_restr0.0101313
X-RAY DIFFRACTIONf_dihedral_angle_d13.1386628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.040.38971120.38332393X-RAY DIFFRACTION51.45
1.04-1.050.33931660.35512908X-RAY DIFFRACTION62.33
1.05-1.070.34522250.34713669X-RAY DIFFRACTION78.44
1.07-1.080.34792240.32214147X-RAY DIFFRACTION89.22
1.08-1.090.31382370.29854219X-RAY DIFFRACTION90.44
1.09-1.110.27572540.28254308X-RAY DIFFRACTION92.07
1.11-1.130.28292250.25274282X-RAY DIFFRACTION92.89
1.13-1.140.22542150.2374450X-RAY DIFFRACTION93.11
1.14-1.160.22142060.21244332X-RAY DIFFRACTION93.05
1.16-1.180.20882420.19444319X-RAY DIFFRACTION92.25
1.18-1.20.20552110.18974362X-RAY DIFFRACTION94.37
1.2-1.220.21252260.16864282X-RAY DIFFRACTION90.85
1.22-1.240.16722690.16084252X-RAY DIFFRACTION92.36
1.24-1.270.16791720.14994091X-RAY DIFFRACTION85.96
1.27-1.30.16212180.14164156X-RAY DIFFRACTION88.85
1.3-1.330.16732500.1314376X-RAY DIFFRACTION94.16
1.33-1.360.18262560.11564459X-RAY DIFFRACTION95.79
1.36-1.40.1512320.10554453X-RAY DIFFRACTION95.15
1.4-1.440.13742240.09964451X-RAY DIFFRACTION95.7
1.44-1.490.11852470.08754437X-RAY DIFFRACTION94.91
1.49-1.540.12142480.08454483X-RAY DIFFRACTION95.83
1.54-1.60.12332200.08414447X-RAY DIFFRACTION95.5
1.6-1.670.11312650.07984417X-RAY DIFFRACTION94.17
1.67-1.760.11891710.08534076X-RAY DIFFRACTION86.53
1.76-1.870.11242310.08334498X-RAY DIFFRACTION95.88
1.87-2.020.11921980.08944575X-RAY DIFFRACTION96.84
2.02-2.220.11312550.09564547X-RAY DIFFRACTION98.18
2.22-2.540.13122530.11664536X-RAY DIFFRACTION97.1
2.54-3.20.17242160.13394433X-RAY DIFFRACTION94.28
3.2-21.060.14551990.13434392X-RAY DIFFRACTION93.28

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