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- PDB-7ki8: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7ki8
TitleCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001580
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SSGCID / SDDC / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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 / Chem-WFA / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001580
Authors: Abendroth, J.A. / Dranow, D.M. / Zigweid, R.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,1943
Polymers19,0361
Non-polymers1,1582
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.460, 70.860, 36.160
Angle α, β, γ (deg.)90.000, 111.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrofolate reductase


Mass: 19035.619 Da / Num. of mol.: 1 / Mutation: C89S, E96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria)
Strain: Agy99 / Gene: dfrA, MUL_2179 / Plasmid: MyulA.01062.a.B13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0PQG8, dihydrofolate reductase
#2: 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
#3: Chemical ChemComp-WFA / 1-[2-({3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propyl}amino)phenyl]piperidine-4-carboxylic acid


Mass: 414.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Microlytic Morpheus screen, condition A5: 10% (w/V) PEG 20000, 20% (v/v) PEG MME 550: 30mM each MgCl2, CaCl2: 100mM MES / imidazole pH 6.5: MyulA.01062.a.B13.PS38558 at 7.98mg/ml + 2.5mM ...Details: Microlytic Morpheus screen, condition A5: 10% (w/V) PEG 20000, 20% (v/v) PEG MME 550: 30mM each MgCl2, CaCl2: 100mM MES / imidazole pH 6.5: MyulA.01062.a.B13.PS38558 at 7.98mg/ml + 2.5mM NADP + 2.5mM SDDC-0001580): tray 318200 A1: cryo: direct: puck ucx6-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.25→33.66 Å / Num. obs: 38062 / % possible obs: 99.5 % / Redundancy: 3.639 % / Biso Wilson estimate: 16.438 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.066 / Χ2: 0.943 / Net I/σ(I): 12.65 / Num. measured all: 138500
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.282.9560.4242.388203283627750.7740.52297.8
1.28-1.323.5650.3733.189669271227120.8750.44100
1.32-1.363.6420.3323.779747268526760.90.3999.7
1.36-1.43.660.2714.549550261426090.940.31899.8
1.4-1.443.6680.2135.659127249224880.9560.24999.8
1.44-1.493.6850.186.748962244524320.9660.21199.5
1.49-1.553.6990.1468.198667234723430.9780.17199.8
1.55-1.613.7080.11910.228302224222390.9840.1499.9
1.61-1.693.7120.10311.598066218621730.9870.1299.4
1.69-1.773.710.08713.57657206620640.990.10199.9
1.77-1.863.720.06816.717395199319880.9930.0899.7
1.86-1.983.7150.05819.026910186718600.9960.06899.6
1.98-2.113.7250.05221.726548176517580.9950.06199.6
2.11-2.283.7430.04823.576093164316280.9960.05699.1
2.28-2.53.7370.04425.175590150314960.9960.05299.5
2.5-2.83.7570.04326.025061135313470.9960.0599.6
2.8-3.233.7490.03928.064562122412170.9970.04699.4
3.23-3.953.7550.03929.123815101910160.9960.04699.7
3.95-5.593.7390.03530.0929657987930.9970.04199.4
5.59-33.663.5960.03829.4516114564480.9960.04598.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc2refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NAD and P218-bound structure, PDB entry 6uww

6uww


Resolution: 1.25→33.66 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1586 1926 5.06 %0
Rwork0.1327 36133 --
obs0.134 38059 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.42 Å2 / Biso mean: 16.1988 Å2 / Biso min: 6.61 Å2
Refinement stepCycle: final / Resolution: 1.25→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 78 236 1557
Biso mean--12.09 27.61 -
Num. residues----163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.280.22881390.1862535267498
1.28-1.320.21011360.167125632699100
1.32-1.350.20821280.1625942722100
1.35-1.40.19351290.149125872716100
1.4-1.450.1951470.136425632710100
1.45-1.510.18331440.131925832727100
1.51-1.570.16461470.124125532700100
1.57-1.660.14151100.117126032713100
1.66-1.760.15511400.12625672707100
1.76-1.90.18151470.125625852732100
1.9-2.090.15371390.126226052744100
2.09-2.390.1661320.128725732705100
2.39-3.010.14761300.146226092739100
3.01-33.660.13161580.122626132771100

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