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- PDB-8g4z: E. coli DHFR complex with NADP+ and folate: EF-X off model by Lau... -

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Basic information

Entry
Database: PDB / ID: 8g4z
TitleE. coli DHFR complex with NADP+ and folate: EF-X off model by Laue diffraction (no electric field)
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
FOLIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsGreisman, J.B. / Dalton, K.M. / Brookner, D.E. / Klureza, M.A. / Hekstra, D.R.
Funding support United States, 4items
OrganizationGrant numberCountry
Searle Scholars ProgramSSP-2018-3240
George W. Merck Fund in the New York Community Trust338034
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
DepositionFeb 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2024Provider: 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5118
Polymers18,0511
Non-polymers1,4597
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.286, 45.530, 98.995
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 (E. coli) / Strain: K-12 / 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
#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.: 5 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.14 Å3/Da / Density % sol: 42.53 %
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: 278 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.02-1.18
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Apr 2, 2021
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
21.181
ReflectionResolution: 1.7→41.36 Å / Num. obs: 17637 / % possible obs: 99.5 % / Redundancy: 35.53 % / Biso Wilson estimate: 1.27 Å2 / CC1/2: 0.991 / CC star: 0.998 / Net I/σ(I): 19.68
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 27.4 % / Mean I/σ(I) obs: 9.76 / Num. unique obs: 1702 / CC1/2: 0.957 / CC star: 0.989 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Precognition5.2.2data reduction
careless0.2.0data scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→41.36 Å / SU ML: 0.1333 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 18.217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1953 882 5 %
Rwork0.1471 16755 -
obs0.1495 17637 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.53 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 85 131 1486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421591
X-RAY DIFFRACTIONf_angle_d0.76672197
X-RAY DIFFRACTIONf_chiral_restr0.0533220
X-RAY DIFFRACTIONf_plane_restr0.0068292
X-RAY DIFFRACTIONf_dihedral_angle_d13.2222589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.1891440.14082741X-RAY DIFFRACTION99.45
1.81-1.950.19821440.13422734X-RAY DIFFRACTION99.55
1.95-2.140.17241450.13362755X-RAY DIFFRACTION99.32
2.14-2.450.18141460.1442777X-RAY DIFFRACTION99.63
2.45-3.090.21061480.15632805X-RAY DIFFRACTION99.43
3.09-41.360.20851550.16032943X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: 23.467974335 Å / Origin y: 21.3847718853 Å / Origin z: 35.4667814864 Å
111213212223313233
T-0.0112622713965 Å2-0.0213282461716 Å2-0.0169417597072 Å2--0.0137920609582 Å2-0.0235771068303 Å2---0.0131833495804 Å2
L0.0840342354326 °20.0363537572983 °20.017644101858 °2-0.0304597762995 °2-0.0065095685954 °2--0.0183696172614 °2
S0.000322850147533 Å °0.0313044526767 Å °-0.0209201757653 Å °0.00185654511709 Å °0.013471091942 Å °0.00691712183197 Å °-0.00494201287597 Å °-0.00486246769323 Å °0.114530754344 Å °
Refinement TLS groupSelection details: all

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