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- PDB-8dai: E. coli DHFR complex with NADP+ and 10-methylfolate -

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Basic information

Entry
Database: PDB / ID: 8dai
TitleE. coli DHFR complex with NADP+ and 10-methylfolate
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 / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / 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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / methopterin / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.14 Å
AuthorsGreisman, J.B. / 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
DepositionJun 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 8, 2023Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Jul 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 1.4Nov 13, 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)19,4707
Polymers18,0511
Non-polymers1,4196
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.251, 45.357, 98.845
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-R6F / methopterin / N-(4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl)methyl](methyl)amino}benzoyl)-L-glutamic acid / 10-methylfolic acid


Mass: 455.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7O6 / 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
#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.: 172 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 mM imadazole (pH 5.4-5.8), 15-20% PEG 400, 125 mM MnCl2
PH range: 5.4 - 5.8

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Data collection

DiffractionMean temperature: 285 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.953692 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: May 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953692 Å / Relative weight: 1
ReflectionResolution: 1.14→49.42 Å / Num. obs: 105471 / % possible obs: 96.28 % / Redundancy: 25.9 % / Biso Wilson estimate: 15.57 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1477 / Rpim(I) all: 0.02843 / Net I/σ(I): 8.62
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 14.9 % / Rmerge(I) obs: 3.344 / Mean I/σ(I) obs: 0.35 / Num. unique obs: 8518 / CC1/2: 0.269 / CC star: 0.651 / Rpim(I) all: 0.8785 / % possible all: 70.65

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Processing

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

7lvc


Resolution: 1.14→49.42 Å / SU ML: 0.1468 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.3611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.16 5171 4.95 %
Rwork0.1268 99294 -
obs0.1284 104465 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.97 Å2
Refinement stepCycle: LAST / Resolution: 1.14→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 85 172 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01341683
X-RAY DIFFRACTIONf_angle_d1.3572328
X-RAY DIFFRACTIONf_chiral_restr0.0959234
X-RAY DIFFRACTIONf_plane_restr0.0115312
X-RAY DIFFRACTIONf_dihedral_angle_d13.979631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.34281080.352033X-RAY DIFFRACTION60.31
1.15-1.170.34661320.32432421X-RAY DIFFRACTION70.47
1.17-1.180.30761390.33222818X-RAY DIFFRACTION81.01
1.18-1.20.35341540.31413057X-RAY DIFFRACTION89.34
1.2-1.210.32371660.30753270X-RAY DIFFRACTION95.07
1.21-1.230.31251860.29323334X-RAY DIFFRACTION96.57
1.23-1.250.27982150.27053373X-RAY DIFFRACTION99.94
1.25-1.260.27031440.25043516X-RAY DIFFRACTION99.95
1.26-1.280.29841830.24763386X-RAY DIFFRACTION99.97
1.28-1.30.27011770.22553420X-RAY DIFFRACTION99.97
1.3-1.330.24252080.20583443X-RAY DIFFRACTION99.81
1.33-1.350.24241800.19183423X-RAY DIFFRACTION99.89
1.35-1.380.23611840.18053435X-RAY DIFFRACTION99.81
1.38-1.410.22731770.17393388X-RAY DIFFRACTION99.89
1.41-1.440.17461790.15513454X-RAY DIFFRACTION100
1.44-1.470.18952020.15173451X-RAY DIFFRACTION99.78
1.47-1.510.16191700.13893426X-RAY DIFFRACTION99.86
1.51-1.550.20941900.13423410X-RAY DIFFRACTION99.97
1.55-1.590.14791770.10573432X-RAY DIFFRACTION99.83
1.59-1.640.14242070.09673419X-RAY DIFFRACTION99.92
1.64-1.70.14571890.09463419X-RAY DIFFRACTION99.75
1.7-1.770.1211360.08863482X-RAY DIFFRACTION99.89
1.77-1.850.13311670.09063431X-RAY DIFFRACTION100
1.85-1.950.11571620.08123483X-RAY DIFFRACTION99.73
1.95-2.070.12521500.08313421X-RAY DIFFRACTION99.61
2.07-2.230.11952090.08743426X-RAY DIFFRACTION99.89
2.23-2.460.13421920.09533433X-RAY DIFFRACTION99.92
2.46-2.810.14011670.11553429X-RAY DIFFRACTION99.67
2.81-3.540.1541610.12063453X-RAY DIFFRACTION99.75
3.54-49.420.14511600.1273408X-RAY DIFFRACTION98.65

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