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- PDB-5sd1: Crystal Structure of Dihydrofolate Reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 5sd1
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1235 (enantiomer)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Mycobacterium tuberculosis / DHFR / NADP / Folate / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 / 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
FORMIC ACID / Chem-I6J / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1235 (enantiomer)
Authors: Mayclin, S.J. / Fairman, J.W. / Dranow, D.M. / Conrady, D.G. / Fox III, D. / Lukacs, C.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. / Abendroth, J.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Other / Structure summary
Category: pdbx_SG_project / pdbx_database_status / struct_keywords
Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)21,1566
Polymers19,8321
Non-polymers1,3245
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.450, 67.320, 72.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate reductase


Mass: 19832.365 Da / Num. of mol.: 1 / Fragment: MtDHFR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: folA, dfrA, Rv2763c, MTV002.28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WNX1, dihydrofolate reductase

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Non-polymers , 5 types, 144 molecules

#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-I6J / (2S)-2-[(2-{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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.8 Å3/Da / Density % sol: 32 % / Mosaicity: 0.165 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MCSG2 B6 (291345b6): 200mM sodium formate, 20% (w/v) PEG3350, 10mg/mL protein conc., cryo 15% ethylene glycol, puck pwp0-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10105 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.356 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.118 / Χ2: 0.944 / Net I/σ(I): 11.01 / Num. measured all: 54263
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.050.3913.2722897446490.8680.45687.2
2.05-2.110.3324.1527917316920.9080.3894.7
2.11-2.170.2725.5333646916910.9510.305100
2.17-2.240.2696.1438206836830.9590.297100
2.24-2.310.2297.0838946596590.9790.251100
2.31-2.390.2077.7237506386380.9780.227100
2.39-2.480.1818.435246326320.9810.199100
2.48-2.580.1639.6933965915910.9850.18100
2.58-2.70.14710.7335125905900.9860.162100
2.7-2.830.12511.6332055455450.9870.138100
2.83-2.980.11112.7530045285270.990.12299.8
2.98-3.160.114.1727944974970.990.11100
3.16-3.380.0915.9927914844830.9920.09999.8
3.38-3.650.07718.4925364384380.9940.084100
3.65-40.07119.2722254064040.9950.07899.5
4-4.470.06520.320803803790.9920.07399.7
4.47-5.160.06721.1419443433430.9950.074100
5.16-6.320.07518.0714872862860.9940.083100
6.32-8.940.07719.4412502362360.9940.085100
8.940.07120.286071441420.9870.08198.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_3874refinement
PDB_EXTRACT3.22data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.15 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 987 9.77 %
Rwork0.1477 9118 -
obs0.1541 10105 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.03 Å2 / Biso mean: 19.7524 Å2 / Biso min: 8.05 Å2
Refinement stepCycle: final / Resolution: 2→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 117 139 1559
Biso mean--18.63 26.26 -
Num. residues----169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.110.24631160.17961207132391
2.11-2.240.28011360.160912691405100
2.24-2.410.23161400.164112981438100
2.41-2.650.2341450.160113001445100
2.65-3.040.23931430.158813021445100
3.04-3.820.19651430.13513391482100
3.82-36.150.16891640.1314031567100
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)
10.14130.02510.68990.9324-1.6697.0005-0.10490.0820.00090.1279-0.0638-0.1387-0.69210.24170.12170.17130.0052-0.02240.1780.02230.18814.377814.16136.6281
22.99641.24591.15044.83421.59192.75040.2342-0.2914-0.29270.4215-0.1037-0.13340.3309-0.0951-0.09910.1792-0.02610.00640.10530.01650.127311.1297-0.2523.3098
37.8204-2.2737-4.00783.5829-0.68453.546-0.0687-0.0363-0.1612-0.0710.06060.26860.366-0.5051-0.01890.1059-0.039600.1385-0.02310.12752.72528.354514.3181
43.2697-0.11640.41565.9972-0.55683.49530.18830.014-0.189-0.0947-0.05990.24680.2428-0.1658-0.1090.08730.0019-0.01030.0924-0.00350.0947.9351-1.81586.6277
53.6264-1.21070.05146.1695-0.51332.72020.02170.176-0.0804-0.2568-0.0598-0.45260.08080.19450.05010.15110.01710.00550.1431-0.00930.147616.8596-2.82190.1786
62.78330.5251-1.7652.68660.30282.54970.03390.07030.0378-0.15120.045-0.0415-0.04240.0178-0.10630.0897-0.0131-0.0280.0830.00020.090116.61268.784311.0623
78.0563-7.5888-4.53827.1744.25782.5619-0.5182-0.2266-0.36490.77040.28170.19450.37630.16480.21580.32360.0219-0.06560.2040.07570.323316.5638-0.01628.9203
82.3642.1284-3.08838.5989-1.53914.62180.1341-0.26150.0682-0.0246-0.0661-0.8058-0.21060.3182-0.04210.1188-0.0244-0.05310.15-0.0270.124121.252314.263618.0977
95.6770.5132-3.44731.2407-0.43552.80140.1511-0.03880.2939-0.01490.0570.13740.0264-0.1042-0.19260.1257-0.0189-0.03110.1409-0.00390.09828.266614.315423.275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 9 )A-9 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 24 )A10 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 35 )A25 - 35
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 61 )A36 - 61
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 89 )A62 - 89
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 115 )A90 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 125 )A116 - 125
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 139 )A126 - 139
9X-RAY DIFFRACTION9chain 'A' and (resid 140 through 159 )A140 - 159

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