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- PDB-7fps: DHFR:NADP+:FOL complex at 290 K (crystal 2) -

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Basic information

Entry
Database: PDB / ID: 7fps
TitleDHFR:NADP+:FOL complex at 290 K (crystal 2)
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: 1.26 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 10, 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 16, 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4567
Polymers18,0511
Non-polymers1,4056
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)34.192, 45.556, 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


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.: 4 / 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: 42.44 %
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: 290 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: 1.26→49.53 Å / Num. obs: 80476 / % possible obs: 99.8 % / Redundancy: 26.7 % / Biso Wilson estimate: 15.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.532 / Rpim(I) all: 0.105 / Net I/σ(I): 18.6
Reflection shellResolution: 1.26→1.28 Å / % possible obs: 98.4 % / Redundancy: 23.3 % / Rmerge(I) obs: 8.097 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3665 / CC1/2: 0.357 / Rpim(I) all: 1.704

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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: 1.26→27.35 Å / SU ML: 0.135 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.5994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1665 3894 4.93 %
Rwork0.1317 75103 -
obs0.1333 78997 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.82 Å2
Refinement stepCycle: LAST / Resolution: 1.26→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 84 165 1519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911700
X-RAY DIFFRACTIONf_angle_d1.08252351
X-RAY DIFFRACTIONf_chiral_restr0.0898233
X-RAY DIFFRACTIONf_plane_restr0.0095313
X-RAY DIFFRACTIONf_dihedral_angle_d13.4292628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.280.28481210.26422331X-RAY DIFFRACTION85.08
1.28-1.290.31741300.26282419X-RAY DIFFRACTION89.44
1.29-1.310.26741330.24062603X-RAY DIFFRACTION93.83
1.31-1.330.27771550.22042622X-RAY DIFFRACTION96.22
1.33-1.350.28041320.21182623X-RAY DIFFRACTION96.63
1.35-1.370.24951530.21222678X-RAY DIFFRACTION97.29
1.37-1.390.25011400.20082684X-RAY DIFFRACTION97.51
1.39-1.410.25691380.20352652X-RAY DIFFRACTION97.69
1.41-1.430.22261470.19052704X-RAY DIFFRACTION98.07
1.43-1.460.22861530.19132695X-RAY DIFFRACTION98.14
1.46-1.490.25891360.17152685X-RAY DIFFRACTION98.91
1.49-1.520.22171530.16662706X-RAY DIFFRACTION99.13
1.52-1.550.2041430.15622750X-RAY DIFFRACTION99.79
1.55-1.590.18751570.1472705X-RAY DIFFRACTION99.69
1.59-1.630.18871510.13452799X-RAY DIFFRACTION99.8
1.63-1.670.19611540.13862666X-RAY DIFFRACTION99.23
1.67-1.720.17531280.13982705X-RAY DIFFRACTION99.13
1.72-1.780.14551140.14052689X-RAY DIFFRACTION96.76
1.78-1.840.15571340.11632748X-RAY DIFFRACTION99.83
1.84-1.910.14391300.10562755X-RAY DIFFRACTION99.79
1.91-20.1471230.10232727X-RAY DIFFRACTION99.82
2-2.110.1191460.12773X-RAY DIFFRACTION99.86
2.11-2.240.12891540.10072691X-RAY DIFFRACTION99.89
2.24-2.410.13441480.10262731X-RAY DIFFRACTION99.93
2.41-2.650.15341280.12222775X-RAY DIFFRACTION100
2.65-3.040.18821430.12292727X-RAY DIFFRACTION99.86
3.04-3.820.16211150.12042738X-RAY DIFFRACTION98.62
3.82-27.350.13731350.13562722X-RAY DIFFRACTION99.2

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