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

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Basic information

Entry
Database: PDB / ID: 5sco
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-M7
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
BROMIDE ION / Chem-GQO / 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-M7
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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3197
Polymers19,8321
Non-polymers1,4876
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.300, 67.410, 78.330
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-GQO / 2-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-N,N-dimethylethane-1-sulfonamide


Mass: 423.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H29N5O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.95 Å3/Da / Density % sol: 36.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Wizard 3/4 condition G1: 0.15 M potassium bromide, 30% PEG2000 MME

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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: Apr 16, 2015 / Details: Diamond [111]
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: 39019 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.792 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.055 / Net I/σ(I): 20.56 / Num. measured all: 249141
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
1.3-1.330.7470.5032.48922287628440.60898.9
1.33-1.370.8480.4483.2911127274127410.517100
1.37-1.410.9090.4134.4114554270927090.458100
1.41-1.450.9590.3186.1316075261626160.348100
1.45-1.50.9750.2737.8417793253925390.295100
1.5-1.550.9840.2110.0317534245724570.227100
1.55-1.610.9910.15712.8617161239323930.169100
1.61-1.680.9930.13114.8916538229822980.141100
1.68-1.750.9960.10118.3715937221222120.109100
1.75-1.840.9970.07822.2715282211521150.084100
1.84-1.940.9980.06227.8714497202320230.067100
1.94-2.060.9980.05132.0113591189218920.055100
2.06-2.20.9980.04436.2912900180618060.048100
2.2-2.370.9990.04138.711984168816870.04599.9
2.37-2.60.9990.03742.0611067155915580.0499.9
2.6-2.910.9990.03444.999940142114210.037100
2.91-3.360.9990.0348.878713126612650.03399.9
3.36-4.110.9990.02950.587207108410830.03299.9
4.11-5.810.9990.03150.3654498608600.033100
5.810.9990.03147.7528705145000.03597.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_1932refinement
PDB_EXTRACT3.11data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→30.96 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 1950 5 %
Rwork0.1649 37067 -
obs0.1666 39017 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.19 Å2 / Biso mean: 15.0787 Å2 / Biso min: 6.34 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 81 202 1572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131425
X-RAY DIFFRACTIONf_angle_d1.5541956
X-RAY DIFFRACTIONf_chiral_restr0.071206
X-RAY DIFFRACTIONf_plane_restr0.009245
X-RAY DIFFRACTIONf_dihedral_angle_d21.256528
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 (%)
1.3-1.33250.23211370.20662605274299
1.3325-1.36850.24611350.183425752710100
1.3685-1.40880.22861370.161726062743100
1.4088-1.45420.22781380.14926252763100
1.4542-1.50620.18551370.143726022739100
1.5062-1.56650.20571380.138726352773100
1.5665-1.63780.16481390.133226232762100
1.6378-1.72420.21131380.140526362774100
1.7242-1.83220.21621390.151526342773100
1.8322-1.97360.18161390.151226332772100
1.9736-2.17220.19811390.156626652804100
2.1722-2.48640.20441420.170126752817100
2.4864-3.13210.20551420.188727122854100
3.1321-30.96920.19011500.172128412991100

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