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- PDB-8g50: E. coli DHFR complex with NADP+ and folate: EF-X excited state mo... -

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Basic information

Entry
Database: PDB / ID: 8g50
TitleE. coli DHFR complex with NADP+ and folate: EF-X excited state model by Laue diffraction (electric field along b axis; 8-fold extrapolation of structure factor differences)
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 1.2Nov 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,02216
Polymers36,1032
Non-polymers2,91914
Water4,486249
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5669
Polymers18,0511
Non-polymers1,5148
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4567
Polymers18,0511
Non-polymers1,4056
Water181
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 number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Dihydrofolate reductase


Mass: 18051.338 Da / Num. of mol.: 2
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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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
Reflection

Entry-ID: 8G50 / CC star: 0.997 / Diffraction-ID: 1 / % possible obs: 99.4 %

Resolution (Å)Num. obsRedundancy (%)Biso Wilson estimate (Å2)CC1/2Net I/σ(I)
1.7-41.363367118.63-5.080.98714.27
1.7-41.363367118.350.98914.42
1.7-49.53366918.340.98814.42
Reflection shell

Diffraction-ID: 1 / % possible all: 99.5 / Resolution: 1.7→1.76 Å

Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2CC star
14.16732920.9270.981
13.736.9332910.9290.981
13.686.9132920.9290.982

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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: 0.3158 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 37.698
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3501 1694 5.03 %
Rwork0.3064 31953 -
obs0.3086 33647 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.54 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 170 249 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862959
X-RAY DIFFRACTIONf_angle_d0.78114071
X-RAY DIFFRACTIONf_chiral_restr0.0578420
X-RAY DIFFRACTIONf_plane_restr0.0061530
X-RAY DIFFRACTIONf_dihedral_angle_d12.91531074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.49931370.43012638X-RAY DIFFRACTION99.25
1.75-1.810.44811390.41622664X-RAY DIFFRACTION99.33
1.81-1.870.42631400.37452628X-RAY DIFFRACTION99.57
1.87-1.950.42611390.35952648X-RAY DIFFRACTION99.43
1.95-2.030.39821420.33792651X-RAY DIFFRACTION99.43
2.03-2.140.36191400.31232650X-RAY DIFFRACTION99.15
2.14-2.280.34081400.29362688X-RAY DIFFRACTION99.72
2.28-2.450.35881430.29682631X-RAY DIFFRACTION99.43
2.45-2.70.32591380.2642652X-RAY DIFFRACTION99.29
2.7-3.090.26921410.23722692X-RAY DIFFRACTION99.58
3.09-3.890.23221470.20672684X-RAY DIFFRACTION99.58
3.89-41.360.2561480.23832727X-RAY DIFFRACTION98.63
Refinement TLS params.Method: refined / Origin x: 14.9732027231 Å / Origin y: 34.1065930665 Å / Origin z: 24.8020526262 Å
111213212223313233
T0.00728886003936 Å2-0.00921708824204 Å2-0.00547277780371 Å2-0.011116723143 Å20.00568327891725 Å2--0.00837246126194 Å2
L0.0757003141036 °2-0.0522361124494 °2-0.0454546322571 °2-0.170056836211 °20.0921736649295 °2--0.133484710702 °2
S-0.0019037497057 Å °0.0125810501326 Å °-0.00864028751435 Å °0.000275959881141 Å °0.00766258625457 Å °0.0152535319201 Å °0.000682659543744 Å °-0.0129636452343 Å °0.00684824555069 Å °
Refinement TLS groupSelection details: all

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