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- PDB-7km7: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7km7
TitleCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, tetragonal crystal from
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 metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / 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
BROMIDE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-WPD / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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-0001914, tetragonal crystal form
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 2, 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)20,4075
Polymers19,0941
Non-polymers1,3144
Water2,702150
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)59.130, 59.130, 129.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-203-

BR

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Components

#1: Protein Dihydrofolate reductase


Mass: 19093.654 Da / Num. of mol.: 1 / Mutation: C89S
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
#3: Chemical ChemComp-WPD / (2S)-2-[(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid


Mass: 410.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen condition b1: 10% (w/V) PEG 20,000, 20% (V/V) PEG MME 550: 30mM each sodium fluoride, sodium bromide, sodium iodide: 100m MES / imidazole HCl pH 6.5: MyulA.01062.a.B11. ...Details: Morpheus screen condition b1: 10% (w/V) PEG 20,000, 20% (V/V) PEG MME 550: 30mM each sodium fluoride, sodium bromide, sodium iodide: 100m MES / imidazole HCl pH 6.5: MyulA.01062.a.B11.PS38525 at 12.52mg/ml + 2.5 mM NADP and SDDC-0001914 (bsi111353): tray 318485b1: cryo: direct: puck poq5-1

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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 22, 2020
RadiationProtocol: 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: 22100 / % possible obs: 99.7 % / Redundancy: 9.298 % / Biso Wilson estimate: 38.347 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.042 / Χ2: 0.932 / Net I/σ(I): 28.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.858.3360.5893.4916110.9510.62799.3
1.85-1.99.4210.4654.9215450.9680.491100
1.9-1.959.6010.3566.5415190.9780.375100
1.95-2.019.6090.2628.514700.9910.276100
2.01-2.089.5880.19411.4414280.9930.205100
2.08-2.159.5850.13715.6313830.9960.145100
2.15-2.239.5440.12317.3713510.9960.13100
2.23-2.329.5240.10520.0812960.9970.111100
2.32-2.439.5940.07526.512390.9980.079100
2.43-2.559.4830.06231.1412100.9990.065100
2.55-2.689.5080.05337.1511400.9990.05699.9
2.68-2.859.3740.04641.4110800.9990.048100
2.85-3.049.3310.03747.9510190.9990.03999.9
3.04-3.299.2690.03454.659720.9990.03699.9
3.29-3.69.1770.03159.298770.9990.03299.3
3.6-4.029.1320.02762.358090.9990.02999.5
4.02-4.658.960.02665.3573110.02899.2
4.65-5.698.8540.02665.1761810.02798.9
5.69-8.058.2490.02861.0149810.02998.4
8.05-507.2070.02859.683040.9990.0392.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NAD and P218-bound structure, PDB entry 6uww

6uww


Resolution: 1.8→43.66 Å / SU ML: 0.2411 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2003 9.08 %0
Rwork0.1773 20055 --
obs0.1801 22058 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 79 150 1440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811343
X-RAY DIFFRACTIONf_angle_d0.96131843
X-RAY DIFFRACTIONf_chiral_restr0.0606202
X-RAY DIFFRACTIONf_plane_restr0.0087251
X-RAY DIFFRACTIONf_dihedral_angle_d14.2579506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.34771420.32521383X-RAY DIFFRACTION98.83
1.85-1.890.33241400.27451396X-RAY DIFFRACTION99.87
1.9-1.950.30531450.22741408X-RAY DIFFRACTION99.81
1.95-2.010.25121260.20941406X-RAY DIFFRACTION99.8
2.01-2.090.23941370.20511411X-RAY DIFFRACTION100
2.09-2.170.2341400.19131414X-RAY DIFFRACTION100
2.17-2.270.26761660.20651402X-RAY DIFFRACTION100
2.27-2.390.2491500.20411396X-RAY DIFFRACTION100
2.39-2.540.23611420.18521439X-RAY DIFFRACTION100
2.54-2.730.22951410.18661425X-RAY DIFFRACTION99.94
2.73-3.010.21161460.19751441X-RAY DIFFRACTION100
3.01-3.440.23571320.17121471X-RAY DIFFRACTION99.81
3.44-4.340.14851380.14611481X-RAY DIFFRACTION99.63
4.34-43.660.1761580.15451582X-RAY DIFFRACTION98.86
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)
15.642894197420.2829807359180.5790739581815.309733441810.6279896930540.1436752107810.273206386738-0.251627638247-0.5212774647930.0602933601489-0.290550905998-0.2345860948290.08356929228210.275297584567-0.03811538598010.175510458748-0.0102059277954-0.06553768776280.3364684838250.03153192053070.200815691328-17.754671771516.4218993445-0.326067644409
29.36618406655-4.36607400198-6.980254889755.782807484614.903961978267.679250560970.3109410150280.09723265229720.409812891887-0.3294554065530.00633840869968-0.00946005125284-0.356183164388-0.246969058596-0.3532695527620.2241865600470.0249917514586-0.0384688291130.2866370117780.0260390385920.223157228564-22.067856086126.2326462941-6.92879847299
35.38102815313-0.236233030666-0.1117501493123.24343758121.159356505243.245917072540.2961804441110.795652929788-0.585201989443-0.305684592302-0.2390982449420.0572173557931-0.0826860407824-0.219448670094-0.06508714626790.2102949443890.0896593230431-0.06911716281840.384316844483-0.07748516777050.231460862501-24.692273273414.2958668844-13.6966933259
43.94568142477-3.728543926860.1995291321774.421186928481.522136887383.500753389680.4783563358091.41028695647-1.08799425878-0.3054746470440.0138575947043-0.3028612959210.1746013143030.593820265032-0.4076701224670.3592038452570.128382831448-0.08921520847720.716338127059-0.2688442095210.518136384665-19.34446609747.50320060923-19.668601158
55.0885089178-0.09344422551190.6213706039144.005617077421.587183812742.665574288250.301671475773-0.0368832164597-0.405636783632-0.010790851449-0.110552989231-0.324176814312-0.01734989731360.45752995955-0.1524232616020.1738124748490.0170600301724-0.04372654823920.3680416636860.03851622280650.269787802938-10.613993923416.6716845643-3.67286691441
66.76811916154-3.60459204303-1.515039370157.21992987083.048833445827.210264165220.386590853833-0.1457900853350.242420714165-0.277712587649-0.0985943782936-0.282534899213-0.598488915638-0.325443483918-0.2875470738120.225116002663-0.0670802233424-0.02652082816290.3316735878220.01157141490640.192323047112-14.099583462728.44612158071.33241205998
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 3 through 26 )3 - 261 - 24
22chain 'A' and (resid 27 through 37 )27 - 3725 - 35
33chain 'A' and (resid 38 through 67 )38 - 6736 - 65
44chain 'A' and (resid 68 through 96 )68 - 9666 - 89
55chain 'A' and (resid 97 through 145 )97 - 14590 - 138
66chain 'A' and (resid 146 through 165 )146 - 165139 - 158

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