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

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Basic information

Entry
Database: PDB / ID: 5scx
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1190 (racemic mixture)
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-HJI / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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-1190 (racemic mixture)
Authors: Mayclin, S.J. / Conrady, D.G. / Lorimer, D.D.
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)21,0715
Polymers19,8321
Non-polymers1,2394
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.280, 67.280, 72.290
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, 192 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-HJI / (2R)-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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 0.152 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MCSG3 D4: 200mM NaCl, 100mM imidazole: HCl pH8, 1M potassium sodium tartrate, 10mg/mL, cryo 20% EG, puck uqr1-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 35590 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.013 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.044 / Net I/σ(I): 24.75 / Num. measured all: 212877
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
1.3-1.330.8710.483.5515420264025380.52596.1
1.33-1.370.9140.4074.315207253725230.44599.4
1.37-1.410.9380.354.9514716250024290.38297.2
1.41-1.450.9510.2786.3714375240923770.30498.7
1.45-1.50.9730.2138.2113982234423100.23398.5
1.5-1.550.9790.17310.313431226022130.18997.9
1.55-1.610.990.13512.6813180219321890.14899.8
1.61-1.680.9920.10815.6312712211820900.11898.7
1.68-1.750.9950.08819.0212137202320000.09698.9
1.75-1.840.9970.06823.9611761196819530.07499.2
1.84-1.940.9980.0531.3311260186818670.05599.9
1.94-2.060.9990.04137.610440173917320.04599.6
2.06-2.20.9990.03643.39842165416490.03999.7
2.2-2.370.9990.03246.999238155215510.03599.9
2.37-2.60.9990.02852.028558145214490.03199.8
2.6-2.910.9990.02457.797644130413020.02799.8
2.91-3.3610.02163.596729116211620.023100
3.36-4.1110.01969.335698100710060.02199.9
4.11-5.8110.01769.643387957920.01999.6
5.810.9990.01964.3522094724580.02197

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_2499refinement
PDB_EXTRACT3.11data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→36.145 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1752 1925 5.41 %
Rwork0.1356 33663 -
obs0.1377 35588 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.16 Å2 / Biso mean: 16.864 Å2 / Biso min: 6.38 Å2
Refinement stepCycle: LAST / Resolution: 1.3→36.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 82 188 1598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051499
X-RAY DIFFRACTIONf_angle_d0.8852058
X-RAY DIFFRACTIONf_chiral_restr0.075215
X-RAY DIFFRACTIONf_plane_restr0.006284
X-RAY DIFFRACTIONf_dihedral_angle_d16.144853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3001-1.33260.21661240.16312321244596
1.3326-1.36860.19731470.148623522499100
1.3686-1.40890.23751400.15322318245897
1.4089-1.45440.19621210.13582382250399
1.4544-1.50630.14621430.12452338248199
1.5063-1.56660.15441310.11872388251998
1.5666-1.63790.15261370.11832380251799
1.6379-1.72430.15871380.1192394253299
1.7243-1.83230.15271300.12512413254399
1.8323-1.97380.1481500.12323942544100
1.9738-2.17240.16261520.128724182570100
2.1724-2.48670.1981240.145724722596100
2.4867-3.13270.20161460.151824812627100
3.1327-36.1590.16951420.13452612275499

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