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- PDB-7l9t: Crystal Structure of Dihydrofolate reductase from Mycolicibacteri... -

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Basic information

Entry
Database: PDB / ID: 7l9t
TitleCrystal Structure of Dihydrofolate reductase from Mycolicibacterium smegmatis in complex with SDDC-0001565 inhibitor
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / SSGCID / Dihydrofolate reductase / SDDC-0001565 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-QKJ / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Acetyl-coenzyme A synthetase synthetase from Coccidioides immitis in complex with PRX
Authors: DeBouver, N.D. / Bolejack, M.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 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)19,1045
Polymers18,4731
Non-polymers6314
Water1,45981
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)53.750, 53.750, 107.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

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Components

#1: Protein Dihydrofolate reductase /


Mass: 18472.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: folA, MSMEI_2607 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FC10, dihydrofolate reductase
#2: Chemical ChemComp-QKJ / 3-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid


Mass: 360.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: MysmA.01062.a.B11.PS38260 [Barcode: 309084e9, PuckID: hne4-2, Cryo: 20% EG, Concentration: 8.8 mg/mL] 2 M Ammonium sulfate, 100 mM Sodium phosphate dibasic / Citric acid pH 4.2

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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: Dec 10, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 15341 / % possible obs: 99.9 % / Redundancy: 9.246 % / Biso Wilson estimate: 36.009 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.041 / Χ2: 0.947 / Net I/σ(I): 30.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.858.2350.5153.3811090.9390.548100
1.85-1.99.4830.374510600.9730.39499.8
1.9-1.959.5020.2696.9110420.9890.283100
1.95-2.019.5150.2039.2110280.9940.214100
2.01-2.089.4880.17111.29920.9940.18100
2.08-2.159.5010.13114.859900.9960.138100
2.15-2.239.5090.10519.159160.9970.111100
2.23-2.329.4640.09521.348860.9980.1100
2.32-2.439.4670.07925.518580.9980.083100
2.43-2.559.4190.06331.188290.9980.06699.9
2.55-2.689.5290.05236.097980.9990.055100
2.68-2.859.3420.04740.027460.9990.05100
2.85-3.049.350.03850.017170.9990.04100
3.04-3.299.3050.03259.426620.9990.033100
3.29-3.69.080.02865.7562210.0399.8
3.6-4.029.1420.02373.7156310.025100
4.02-4.659.0530.02177.9150810.02299.4
4.65-5.698.6970.02273.9843510.023100
5.69-8.058.3070.02271.2236210.024100
8.05-506.9590.02370.952180.9990.02594.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4-4035refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CXM

6cxm


Resolution: 1.8→48.08 Å / SU ML: 0.2447 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5953
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 1499 9.82 %
Rwork0.2064 13771 -
obs0.2113 15270 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 40 81 1293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581260
X-RAY DIFFRACTIONf_angle_d0.80531724
X-RAY DIFFRACTIONf_chiral_restr0.0526189
X-RAY DIFFRACTIONf_plane_restr0.0075221
X-RAY DIFFRACTIONf_dihedral_angle_d13.88444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.42451330.33731218X-RAY DIFFRACTION99.93
1.86-1.920.30511350.25841218X-RAY DIFFRACTION99.56
1.92-20.27611280.21531238X-RAY DIFFRACTION99.71
2-2.090.2581310.21141210X-RAY DIFFRACTION99.93
2.09-2.20.26421360.20871222X-RAY DIFFRACTION99.93
2.2-2.340.30111460.22611240X-RAY DIFFRACTION100
2.34-2.520.27111600.20291207X-RAY DIFFRACTION99.93
2.52-2.780.21391190.20781275X-RAY DIFFRACTION99.86
2.78-3.170.31051160.21131287X-RAY DIFFRACTION100
3.18-40.22171480.19171282X-RAY DIFFRACTION99.93
4-48.080.23931470.1941374X-RAY DIFFRACTION99.22
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.33932517357-1.208288432441.397056102093.63200849239-0.2547296240734.281366320530.12827845909-0.149338685992-0.272159010581-0.004448858515460.006127434787360.1971051080310.0604669366512-0.197318888033-0.1152171013660.107749283597-0.01481060537240.00959877315190.155025097462-0.01799657030670.161663965483-13.156210102111.1749831748-13.9976280035
25.389518131271.28882168823-1.076422567635.63873931268-0.7980532433711.991411063420.160564144341-0.275948808731-0.6706810914930.1442232551030.03520819693360.3180894865971.18745080108-0.339638946537-0.1043924035170.499055074097-0.11577778029-0.08601338559070.3131718069560.0754486859740.288698424314-11.0161911978-3.2054099721-9.04739384888
34.748665529821.62622353699-0.2902859036822.6200618256-0.3664268288287.91122408329-0.0109288943388-0.4286821088650.0293613735827-0.0398497371191-0.0006128279572380.158626240368-0.399341401983-0.5939693543890.003733940695280.1762016784010.06245471164250.01687604659960.280410539144-0.02839948640990.243384604275-18.753024425515.5204455917-10.9284720984
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 36 )1 - 361 - 36
22chain 'A' and (resid 37 through 94 )37 - 9437 - 94
33chain 'A' and (resid 95 through 156 )95 - 15695 - 156

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