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

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Basic information

Entry
Database: PDB / ID: 5sct
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-783
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
Chem-H03 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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-783
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)21,0423
Polymers19,8321
Non-polymers1,2102
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.190, 67.170, 72.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer, the same as asu

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Components

#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
#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-H03 / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-N-(dimethylsulfamoyl)propanamide


Mass: 466.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.79 Å3/Da / Density % sol: 31.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MORPHEUS D12: 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 20mM each alcohol (1,6-hexanediol, 1-butanol, (RS)-1,2- propanediol, 2-propanol, 1,4-butanediol, 1,2-propanediol), 100mM bicine/Trizma base pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: FR-E+ Superbright / Wavelength: 1.5418 Å
DetectorType: Saturn 944+ / Detector: CCD / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 21159 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.212 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.062 / Net I/σ(I): 27.62 / Num. measured all: 300836
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.590.8990.3854.488172156414600.42193.4
1.59-1.630.9430.376.2213665150714310.3995
1.63-1.680.970.3047.5914862146114440.31998.8
1.68-1.730.9790.2728.6815115144314060.28597.4
1.73-1.790.9850.21810.7115442138213810.22899.9
1.79-1.850.9910.17413.2715603135513510.18299.7
1.85-1.920.9950.13117.0415788130513040.13799.9
1.92-20.9980.121.8415866124712470.104100
2-2.090.9970.09423.6415965122212220.098100
2.09-2.190.9980.07829.0615696114111410.081100
2.19-2.310.9990.07333.0416728109910960.07599.7
2.31-2.450.9990.07137.3518201107010690.07399.9
2.45-2.620.9990.06342.46173689809780.06599.8
2.62-2.830.9990.05847.02173989259240.05999.9
2.83-3.10.9990.05253.2174118528520.053100
3.1-3.4710.04865.17187407857850.049100
3.47-410.04471.59172946986980.045100
4-4.910.04272.67147776136130.043100
4.9-6.930.9990.04965.82109904664660.05100
6.930.9990.04564.8857552912910.046100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_2196refinement
PDB_EXTRACT3.11data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→49.257 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1807 1053 4.98 %
Rwork0.1553 20105 -
obs0.1566 21158 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.21 Å2 / Biso mean: 16.6543 Å2 / Biso min: 5.03 Å2
Refinement stepCycle: LAST / Resolution: 1.55→49.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 80 163 1572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221500
X-RAY DIFFRACTIONf_angle_d1.5032062
X-RAY DIFFRACTIONf_chiral_restr0.099214
X-RAY DIFFRACTIONf_plane_restr0.008263
X-RAY DIFFRACTIONf_dihedral_angle_d28.765531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5501-1.62070.20691140.1872339245393
1.6207-1.70610.19331410.16392441258298
1.7061-1.8130.1911290.16242492262199
1.813-1.9530.18341290.155124992628100
1.953-2.14960.17991370.153525122649100
2.1496-2.46060.17831270.158725512678100
2.4606-3.10.19051360.158625582694100
3.1-49.28220.16751400.144827132853100
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)
10.42450.46240.05321.2390.2510.06920.01370.07140.1137-0.0803-0.0287-0.044-0.19960.14170.01010.0931-0.00130.00430.11520.02150.096616.131116.62426.8747
20.6659-0.18030.03331.47580.30891.38390.0602-0.0176-0.08420.1016-0.05390.08920.1167-0.11670.00070.0509-0.0221-0.00210.09170.01220.08437.34331.112113.3115
31.1527-0.3702-0.22733.2806-0.44111.89280.04610.1775-0.0031-0.1428-0.0276-0.2480.09190.0135-0.03560.09860.010.00480.1253-0.01150.124216.2119-2.4920.2204
41.25520.3594-0.35581.3811-0.01321.84560.087-0.0165-0.0198-0.0045-0.0318-0.12420.0020.0629-0.06410.039-0.0026-0.0060.06290.01370.06216.46798.844810.9884
51.2944-1.63-0.75372.12770.9150.5268-0.0187-0.3218-0.19320.4158-0.0123-0.11740.13170.2115-0.00660.2817-0.0017-0.04710.22810.06080.182416.7941-0.21128.968
61.60560.8606-0.7431.30680.16041.68370.1552-0.14130.06830.1398-0.0359-0.2764-0.12280.0623-0.10890.0919-0.01050.0040.13580.00430.132720.877314.170918.1735
71.59950.2372-0.74521.15050.0721.53560.2069-0.14120.22770.086-0.03550.1606-0.0435-0.0425-0.07670.0819-0.02760.00410.12640.00350.07848.175514.143823.2659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -13 through 9 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 89 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 90 through 115 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 125 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 139 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 159 )A0

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