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- PDB-5sd4: Crystal Structure of Dihydrofolate Reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 5sd4
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1218
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 / glycine biosynthetic 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-HVR / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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-1218
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)21,2659
Polymers19,8321
Non-polymers1,4338
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.530, 66.920, 72.040
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, 228 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-HVR / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)prop-2-yn-1-ol


Mass: 343.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 0.207 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MCSG4 F7 (295168f7): 200mM Magnesium chloride, 100mM MES:NaOH pH 6.5, 10mg/mL, seeded from 284871d9, cryo 20% EG, puck djl6-7

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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
RadiationMonochromator: C 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 38755 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.122 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.043 / Net I/σ(I): 27.51 / Num. measured all: 279834
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
1.25-1.280.9430.3135.317016299325670.3485.8
1.28-1.320.9650.2726.6419733282526840.29395
1.32-1.360.9730.2467.6819658279326320.26494.2
1.36-1.40.9810.2079.1119306272425890.22295
1.4-1.440.9880.17211.0218734263525160.18595.5
1.44-1.490.9910.13913.4617962253824320.14995.8
1.49-1.550.9940.11716.0717453247723520.12695
1.55-1.610.9950.09419.7416792236522910.10196.9
1.61-1.690.9970.08122.8716102228022140.08797.1
1.69-1.770.9980.06826.6915479220221190.07396.2
1.77-1.860.9990.05233.5714706208820160.05696.6
1.86-1.980.9990.04140.7914003199119390.04597.4
1.98-2.110.9990.03745.5312990185518130.03997.7
2.11-2.280.9990.03349.3712353175317240.03598.3
2.28-2.50.9990.02953.2311272159915770.03198.6
2.5-2.80.9990.02659.7310356147214590.02899.1
2.8-3.2310.02263.359050130612950.02499.2
3.23-3.9510.0268.267638112511120.02198.8
3.95-5.5910.01870.260218958910.0299.6
5.5910.0264.4232105475330.02297.4

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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: 1.25→33.46 Å / Occupancy max: 1 / Occupancy min: 0.09 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1634 2052 5.3 %
Rwork0.1323 36649 -
obs0.134 38701 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.15 Å2 / Biso mean: 16.6904 Å2 / Biso min: 4.76 Å2
Refinement stepCycle: LAST / Resolution: 1.25→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 94 220 1611
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 (%)
1.25-1.27910.2121270.16452140226785
1.2791-1.31110.19771330.14812372250594
1.3111-1.34650.16991260.14192394252094
1.3465-1.38610.17211360.13272358249495
1.3861-1.43090.1811330.12822391252495
1.4309-1.4820.18521330.12492406253995
1.482-1.54140.14751380.12362408254696
1.5414-1.61150.15151490.12572429257897
1.6115-1.69650.1781420.11982444258697
1.6965-1.80280.13861320.12672474260697
1.8028-1.94190.16341280.1262500262897
1.9419-2.13730.16551400.12512492263297
2.1373-2.44650.15561520.13692530268299
2.4465-3.0820.17591480.14032572272099
3.082-33.4720.15071350.13292739287499

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