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- PDB-7km9: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7km9
TitleCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001913, 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


glycine biosynthetic process / 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
BROMIDE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-WPJ / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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-0001913, 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)20,3856
Polymers19,0361
Non-polymers1,3495
Water2,144119
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)58.970, 58.970, 130.340
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 124 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-WPJ / (2R)-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 / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.8 %
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.B13. ...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.B13.PS38558 at 7.98mg/ml + 2.5 mM NADP and SDDC-0001913 (bsi111354): tray 318490b1: cryo: direct: puck poq5-9

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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: 1.95→50 Å / Num. obs: 17565 / % possible obs: 99.9 % / Redundancy: 11.343 % / Biso Wilson estimate: 42.213 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.062 / Χ2: 0.932 / Net I/σ(I): 22.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-211.8420.5614.1112580.9770.587100
2-2.0611.90.4435.6712300.9760.463100
2.06-2.1211.7610.3517.4312160.9830.367100
2.12-2.1811.7540.2649.6211670.990.277100
2.18-2.2511.7070.25710.111290.9870.269100
2.25-2.3311.6740.19812.3810910.9950.20899.9
2.33-2.4211.4750.13916.7310640.9970.146100
2.42-2.5211.3150.11119.4210350.9970.116100
2.52-2.6311.3060.09223.279850.9980.096100
2.63-2.7611.190.08326.049530.9980.087100
2.76-2.9111.1910.07128.848950.9980.07499.8
2.91-3.0811.0590.06533.878660.9980.068100
3.08-3.310.9430.05936.668180.9980.06299.9
3.3-3.5611.0530.05639.397510.9990.059100
3.56-3.911.0420.0540.97110.9990.052100
3.9-4.3611.040.04543.876450.9990.047100
4.36-5.0310.9440.04243.445880.9990.04499.8
5.03-6.1710.8630.03942.474960.9990.041100
6.17-8.7210.2170.03341.4541110.035100
8.72-508.4840.03238.632560.9960.03497

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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: 1.95→43.73 Å / SU ML: 0.2172 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.3933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1804 10.31 %0
Rwork0.1818 15701 --
obs0.185 17505 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.22 Å2
Refinement stepCycle: LAST / Resolution: 1.95→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 80 119 1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681332
X-RAY DIFFRACTIONf_angle_d0.88811828
X-RAY DIFFRACTIONf_chiral_restr0.0554202
X-RAY DIFFRACTIONf_plane_restr0.0068248
X-RAY DIFFRACTIONf_dihedral_angle_d13.4382497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.30761290.28711157X-RAY DIFFRACTION99.31
2-2.060.25551320.22961199X-RAY DIFFRACTION100
2.06-2.130.26091290.2161186X-RAY DIFFRACTION100
2.13-2.20.24551360.21391191X-RAY DIFFRACTION100
2.2-2.290.28081390.22421158X-RAY DIFFRACTION99.92
2.29-2.40.25371490.21511180X-RAY DIFFRACTION100
2.4-2.520.23061440.20891188X-RAY DIFFRACTION99.92
2.52-2.680.26451390.19991216X-RAY DIFFRACTION100
2.68-2.890.24741390.20971185X-RAY DIFFRACTION99.85
2.89-3.180.21131240.19591230X-RAY DIFFRACTION99.93
3.18-3.640.21831420.17861224X-RAY DIFFRACTION100
3.64-4.580.16271610.1421230X-RAY DIFFRACTION100
4.58-43.730.19661410.16141357X-RAY DIFFRACTION99.47
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)
16.64912689935-2.894001943170.8826738554546.862975323841.936264916295.902551153710.201908237409-0.6209823530170.362281836645-0.4617089884980.231983488661-0.320368668929-0.6490844720490.118553634251-0.3227315757540.328836780998-0.1021196256160.01426911136470.4121190312070.01113686612540.230750337151-14.238320176528.47746382971.39132700709
25.07587845923-0.167312008391-0.2942763811443.585819270690.9661007292493.632112749880.3608819102070.0822100527533-0.327651288046-0.11140428424-0.273415262364-0.00930647175768-0.05375411402710.0294462119976-0.0797994941880.1786317032680.0393203947693-0.04595322267520.3105247141350.001916018512260.202471475134-20.051750672217.8964267057-5.64512222748
33.96766381102-1.43093984651-0.62322860372.289216372131.615249058232.72526681590.4832926451411.52680170155-1.04237511649-0.232250314153-0.361943751019-0.04525096440350.194586588995-0.1954715358-0.1181234543140.3248657065680.151069006959-0.08164361709230.674236063591-0.2269586489940.467631682299-23.105795868810.3036823927-17.2102835761
42.270919402910.4997158662610.1879687603388.234759178461.243902087682.391598828360.2766342301931.34798540315-0.599564605326-0.2698914357220.231333684179-0.239962924607-0.09423814666580.300414548019-0.3260880275480.2375592148780.108596244478-0.01125161420630.68863324132-0.03831103198180.262054836991-14.911279685318.0463428335-15.6212727755
55.46961217983-0.116464472219-0.5609166023963.573003437461.695577985612.78412121040.314334169482-0.307278601293-0.3569283005680.0278795108395-0.0490035773341-0.272414569305-0.1290541371620.603580096517-0.2218790788040.213451089139-0.00452599551726-0.06983705225860.4646198540980.04895238805510.290547070079-9.844846443116.6691889474-2.43340536104
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 146 through 165 )146 - 165139 - 158
22chain 'A' and (resid 3 through 51 )3 - 511 - 49
33chain 'A' and (resid 52 through 88 )52 - 8850 - 86
44chain 'A' and (resid 89 through 102 )89 - 10287 - 95
55chain 'A' and (resid 103 through 145 )103 - 14596 - 138

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