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

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Basic information

Entry
Database: PDB / ID: 5scw
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-916
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 / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / 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-H6O / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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-916
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)21,1838
Polymers19,8321
Non-polymers1,3507
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.980, 67.470, 78.960
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

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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, 127 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-H6O / (2S)-4-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)butane-1,2-diol


Mass: 376.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N4O4 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: JCSG+ C2 (267551c2): 20%PEG6000, 100mM Citrate pH4.0, 1000mM Lithium chloride, 3.5mM EBSI5673, protein concentration 40.69mg/mL, cryo 20% EG, puck ros7-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: Rotating Copper Anode / Type: FRE+ Superbright / Wavelength: 1.5418 Å
DetectorType: Saturn 944+ / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20378 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.737 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.063 / Net I/σ(I): 19.04 / Num. measured all: 156429
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
1.6-1.640.4760.6910.88110715947200.92345.2
1.64-1.690.5190.6871.282818154612550.86881.2
1.69-1.740.6430.6451.884494149013670.76291.7
1.74-1.790.8210.5872.787205146014000.65195.9
1.79-1.850.9310.4313.877603141613490.47495.3
1.85-1.910.9290.3335.187691137613350.36597
1.91-1.990.9660.2337.257890134313420.25599.9
1.99-2.070.9710.2018.727861126912640.21999.6
2.07-2.160.9860.14612.748625124512440.15899.9
2.16-2.260.9920.12316.899862117811780.131100
2.26-2.390.9950.10620.0510106111911190.112100
2.39-2.530.9960.09422.3710377107810780.099100
2.53-2.710.9970.0826.6410724101110110.085100
2.71-2.920.9980.07332.22120119469460.076100
2.92-3.20.9990.05840.08114948668660.061100
3.2-3.580.9990.04849.57104507927920.05100
3.58-4.130.9990.03761.991427217210.039100
4.13-5.060.9990.03267.6476916136120.03499.8
5.06-7.160.9990.03658.560654854850.037100
7.1610.02962.4232132962940.03199.3

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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: 1.75→39.48 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 1625 9.74 %
Rwork0.1652 15051 -
obs0.1694 16676 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.77 Å2 / Biso mean: 23.7047 Å2 / Biso min: 9.76 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 86 120 1468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081406
X-RAY DIFFRACTIONf_angle_d1.11927
X-RAY DIFFRACTIONf_chiral_restr0.064204
X-RAY DIFFRACTIONf_plane_restr0.007242
X-RAY DIFFRACTIONf_dihedral_angle_d18.376792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7501-1.80160.28581230.20741218134197
1.8016-1.85970.22981280.19771167129595
1.8597-1.92620.23181230.18541227135098
1.9262-2.00330.23241480.166312391387100
2.0033-2.09450.25511330.16812141347100
2.0945-2.20490.20451240.169312751399100
2.2049-2.3430.21151490.170112381387100
2.343-2.52390.21441350.180612571392100
2.5239-2.77780.22591260.169412701396100
2.7778-3.17960.20931540.16812631417100
3.1796-4.00540.17711500.150612931443100
4.0054-39.490.19191320.151913901522100
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)
10.93020.86481.23675.81745.88317.5848-0.0478-0.10890.32920.05440.01420.0311-0.28160.07750.02920.12320.0018-0.00710.1828-0.06360.172-10.699911.7851-7.1256
21.41530.34620.13441.19760.11423.00770.0790.1468-0.1698-0.0895-0.0278-0.16070.18750.3131-0.03560.08630.0245-0.00360.2028-0.03510.1687-3.7635-0.5388-13.4625
31.4455-0.238-0.59421.3828-0.32322.87360.07510.0305-0.064-0.0674-0.00550.046-0.0068-0.0137-0.07220.0783-0.0192-0.01210.125-0.03860.1323-11.86384.2542-12.6282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 9 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 159 )A0

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