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- PDB-7fpl: DHFR:NADP+:FOL complex at 280 K (crystal 1) -

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Basic information

Entry
Database: PDB / ID: 7fpl
TitleDHFR:NADP+:FOL complex at 280 K (crystal 1)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Dihydrofolate Reductase
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic 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: 1.17 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: To Be Published
Title: DHFR:NADP+:FOL complex at 280 K
Authors: Greisman, J.B. / Dalton, K.M. / Brookner, D.E. / Hekstra, D.R.
History
DepositionSep 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: 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)19,4016
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)34.119, 45.500, 99.050
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 / Folate


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 / Nicotinamide adenine dinucleotide phosphate


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 / Water


Mass: 18.015 Da / Num. of mol.: 165 / 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

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.24 %
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: 1.17→32.26 Å / Num. obs: 98434 / % possible obs: 97.8 % / Redundancy: 28.4 % / Biso Wilson estimate: 16.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.285 / Rpim(I) all: 0.054 / Net I/σ(I): 18
Reflection shellResolution: 1.17→1.19 Å / % possible obs: 96.7 % / Redundancy: 28.4 % / Rmerge(I) obs: 8.42 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4836 / CC1/2: 0.343 / Rpim(I) all: 1.586

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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: 1.17→22.75 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.8001
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1653 4747 4.95 %
Rwork0.1439 91133 -
obs0.1449 95880 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.99 Å2
Refinement stepCycle: LAST / Resolution: 1.17→22.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 83 165 1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651700
X-RAY DIFFRACTIONf_angle_d0.97042351
X-RAY DIFFRACTIONf_chiral_restr0.083233
X-RAY DIFFRACTIONf_plane_restr0.0081313
X-RAY DIFFRACTIONf_dihedral_angle_d13.291628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.180.30211480.3182646X-RAY DIFFRACTION84.41
1.18-1.20.30461290.30282778X-RAY DIFFRACTION85.9
1.2-1.210.31871420.30252726X-RAY DIFFRACTION85.1
1.21-1.230.31011490.30162816X-RAY DIFFRACTION89.01
1.23-1.240.28661840.29852721X-RAY DIFFRACTION87.45
1.24-1.260.25731070.27832904X-RAY DIFFRACTION87.96
1.26-1.280.25981490.26722722X-RAY DIFFRACTION87.26
1.28-1.30.25451540.26342931X-RAY DIFFRACTION91
1.3-1.320.28871820.24332991X-RAY DIFFRACTION95.69
1.32-1.340.27861580.2423118X-RAY DIFFRACTION98.05
1.34-1.360.26181830.24153073X-RAY DIFFRACTION95.6
1.36-1.390.26561550.23233143X-RAY DIFFRACTION99.52
1.39-1.410.23191600.22743091X-RAY DIFFRACTION96.76
1.41-1.440.19851780.20563085X-RAY DIFFRACTION98.82
1.44-1.470.21141700.19533141X-RAY DIFFRACTION97.78
1.47-1.510.19361610.1723142X-RAY DIFFRACTION98.71
1.51-1.550.20591770.16133118X-RAY DIFFRACTION97.8
1.55-1.590.1881660.15183152X-RAY DIFFRACTION99.37
1.59-1.630.15161780.13743102X-RAY DIFFRACTION97.88
1.63-1.690.16961730.13473173X-RAY DIFFRACTION99.85
1.69-1.750.17241370.13423051X-RAY DIFFRACTION95.11
1.75-1.820.13281540.1233112X-RAY DIFFRACTION97.84
1.82-1.90.13941480.10873229X-RAY DIFFRACTION99.15
1.9-20.13141410.10433167X-RAY DIFFRACTION99.61
2-2.130.12161640.10523154X-RAY DIFFRACTION99.55
2.13-2.290.12491860.11473153X-RAY DIFFRACTION99.4
2.29-2.520.13971670.11593158X-RAY DIFFRACTION99.76
2.52-2.880.17341620.133192X-RAY DIFFRACTION99.79
2.88-3.630.1621360.12863145X-RAY DIFFRACTION97.88
3.63-22.750.14251490.13793199X-RAY DIFFRACTION99.76

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