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- PDB-7ki9: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7ki9
TitleCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001912
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


NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / 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 / Chem-WFJ / 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-0001912
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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2063
Polymers19,0361
Non-polymers1,1702
Water3,783210
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)29.430, 70.790, 36.180
Angle α, β, γ (deg.)90.000, 111.480, 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-WFJ / 1-[2-(3-{[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]methyl}azetidin-1-yl)phenyl]piperidine-4-carboxylic acid


Mass: 426.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 33.4 %
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 MOPS / HEPES pH 7.5: MyulA.01062.a.B13.PS38558 at 7.98mg/ml + 2.5mM NADP + ...Details: Microlytic Morpheus screen, condition A5: 10% (w/V) PEG 20000, 20% (v/v) PEG MME 550: 30mM each MgCl2, CaCl2: 100mM MOPS / HEPES pH 7.5: MyulA.01062.a.B13.PS38558 at 7.98mg/ml + 2.5mM NADP + 2.5mM SDDC-0001912 (bsi111355): tray 318201 A5: cryo: direct: puck ucx6-7

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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→35.4 Å / Num. obs: 37934 / % possible obs: 99.4 % / Redundancy: 3.641 % / Biso Wilson estimate: 16.339 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.06 / Χ2: 0.938 / Net I/σ(I): 14.22 / Num. measured all: 138110 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.282.9840.4882.2827560.7280.59997.4
1.28-1.323.570.4322.9227060.8190.51100
1.32-1.363.6430.3783.4126650.8720.44499.7
1.36-1.43.6650.3094.2326160.9060.36399.6
1.4-1.443.6730.2495.1824920.9370.293100
1.44-1.493.6810.2026.3124210.9590.23799.5
1.49-1.553.7040.1587.923440.9740.18499.7
1.55-1.613.7080.1269.9922420.9820.147100
1.61-1.693.720.10811.6621600.9870.12699.4
1.69-1.773.7340.0913.8120630.9910.10599.6
1.77-1.863.7330.06617.7919680.9950.07899.4
1.86-1.983.7270.05521.1118590.9970.06499.5
1.98-2.113.7360.04824.8317430.9960.05699.3
2.11-2.283.7290.0427.7316250.9980.04799
2.28-2.53.7480.03730.5914830.9980.04398.7
2.5-2.83.710.03432.1913400.9980.0499
2.8-3.233.7050.0335.8712060.9980.03598.9
3.23-3.953.7350.02738.4710090.9990.03299.3
3.95-5.593.7110.02540.137900.9990.02999
5.59-35.43.5580.02639.414460.9980.03198.7

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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→35.4 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 1983 5.23 %0
Rwork0.1341 35946 --
obs0.1357 37929 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.76 Å2 / Biso mean: 16.2876 Å2 / Biso min: 5.83 Å2
Refinement stepCycle: final / Resolution: 1.25→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 79 227 1578
Biso mean--12.03 26.1 -
Num. residues----166
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 (%)
1.25-1.280.19121490.18282502265198
1.28-1.320.21981310.1725702701100
1.32-1.350.21441470.163325552702100
1.35-1.40.20361630.153425672730100
1.4-1.450.1791280.137525802708100
1.45-1.510.18061530.129925702723100
1.51-1.570.18071260.120625712697100
1.57-1.660.18751470.122925642711100
1.66-1.760.16561550.131825362691100
1.76-1.90.14471410.129925762717100
1.9-2.090.15741450.123825862731100
2.09-2.390.16061330.12852557269099
2.39-3.010.13341320.14362589272199
3.01-35.40.16241330.12712623275699

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