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- PDB-5sd5: Crystal Structure of Dihydrofolate Reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 5sd5
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1230
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-HWI / IMIDAZOLE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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-1230
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)21,2958
Polymers19,8321
Non-polymers1,4627
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.610, 66.990, 71.990
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, 260 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-HWI / 1-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}-4-methylphenyl)azetidine-3-carboxylic acid


Mass: 401.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 0.127 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MCSG4 F7 (295174f7): 200mM Magnesium chloride, 100mM MES:NaOH pH 6.5, 10mg/mL, seeded from 284871d9, cryo 20% EG, puck djl6-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 45612 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.804 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.071 / Net I/σ(I): 15.37 / Num. measured all: 233499
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
1.2-1.230.820.5672.8716185332633260.635100
1.23-1.260.8610.4933.416505323332300.54999.9
1.26-1.30.8930.4193.9816141317031680.46699.9
1.3-1.340.9220.3614.5715694307130710.402100
1.34-1.390.9390.3155.315347298129780.3599.9
1.39-1.430.9590.266.3314914289128870.28999.9
1.43-1.490.9760.2047.9514395278627820.22699.9
1.49-1.550.9790.179.4513850267826740.18999.9
1.55-1.620.9890.13311.8113416257725760.148100
1.62-1.70.9910.10914.4212803247024670.12199.9
1.7-1.790.9940.0916.9112327236223580.199.8
1.79-1.90.9960.0721.3111634224322410.07799.9
1.9-2.030.9970.05525.910921209720900.06199.7
2.03-2.190.9980.04729.5110125196519610.05299.8
2.19-2.40.9980.04132.059404183318290.04699.8
2.4-2.680.9980.03736.178509166916640.04199.7
2.68-3.10.9980.03239.77421146914630.03599.6
3.1-3.790.9990.02744.496320126812620.0399.5
3.79-5.370.9990.02447.6949289959910.02799.6
5.370.9990.02544.4226606045940.02898.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_2919refinement
PDB_EXTRACT3.11data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→33.495 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1527 2079 4.56 %
Rwork0.1311 43533 -
obs0.1321 45612 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.28 Å2 / Biso mean: 17.3532 Å2 / Biso min: 4.76 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 98 253 1648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1998-1.22780.23711330.182128662999100
1.2278-1.25850.19141430.173828382981100
1.2585-1.29250.2131460.153128773023100
1.2925-1.33050.18851450.150428242969100
1.3305-1.37350.18211370.1428763013100
1.3735-1.42260.17771420.129628663008100
1.4226-1.47950.15241340.124828913025100
1.4795-1.54680.14551370.116628643001100
1.5468-1.62840.14051320.120329023034100
1.6284-1.73040.13961450.120728903035100
1.7304-1.8640.14961380.123929153053100
1.864-2.05160.14921120.122129213033100
2.0516-2.34840.14381230.125829543077100
2.3484-2.95840.15721580.138829563114100
2.9584-33.5080.12711540.12593093324799

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