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- PDB-6e4e: Crystal structure of dihydrofolate reductase from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 6e4e
TitleCrystal structure of dihydrofolate reductase from Staphylococcus aureus MW2 bound to NADP and p218
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/Inhibitor / NIAID / DHFR / folate / folic acid / MMV / inhibitor / malaria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


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, subunit A / Dihydrofolate Reductase, subunit A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of dihydrofolate reductase from Staphylococcus aureus MW2 bound to NADP and p218
Authors: Edwards, T.E. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)21,8403
Polymers20,7371
Non-polymers1,1042
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-3 kcal/mol
Surface area7910 Å2
Unit cell
Length a, b, c (Å)79.000, 79.000, 108.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 20736.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A017, 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-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid


Mass: 360.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: StauA.01062.a.M1.PS02450 at 17.2 mg/mL with 2 mM NADP and 2 mM p218 against Morpheus screen condition A1 10% PEG 10,000, 20% PEG MME 550, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES-imidazole pH 6. ...Details: StauA.01062.a.M1.PS02450 at 17.2 mg/mL with 2 mM NADP and 2 mM p218 against Morpheus screen condition A1 10% PEG 10,000, 20% PEG MME 550, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES-imidazole pH 6.5, crystal tracking ID 299715a1, unique puck ID wan7-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→42.611 Å / Num. obs: 16429 / % possible obs: 100 % / Redundancy: 14.158 % / Biso Wilson estimate: 31.892 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.134 / Χ2: 0.939 / Net I/σ(I): 14.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9514.480.5095.2811740.9610.528100
1.95-214.4860.4366.1711440.9660.452100
2-2.0614.4440.3577.3611310.9760.37100
2.06-2.1214.4480.2998.5610920.9830.31100
2.12-2.1914.410.24110.3910660.9870.25100
2.19-2.2714.4370.21411.5310340.9910.221100
2.27-2.3614.3630.19612.49930.990.203100
2.36-2.4514.4280.18813.279630.9880.195100
2.45-2.5614.3450.16214.879180.990.168100
2.56-2.6914.290.14516.498910.9920.15100
2.69-2.8314.2060.13617.018480.9930.141100
2.83-314.2240.12119.368020.9940.125100
3-3.2114.1060.11520.737630.9950.119100
3.21-3.4713.9930.10822.527150.9950.112100
3.47-3.813.9050.10723.276640.9950.111100
3.8-4.2513.850.10623.786010.9920.111100
4.25-4.9113.3810.10523.995490.990.109100
4.91-6.0113.270.10523.844670.9940.109100
6.01-8.512.4840.10822.923760.9910.112100
8.5-42.61110.7180.11122.152380.9810.11798.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FGG

4fgg


Resolution: 1.9→42.611 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.02
RfactorNum. reflection% reflection
Rfree0.2236 800 4.87 %
Rwork0.1802 --
obs0.1824 16426 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.06 Å2 / Biso mean: 38.5604 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 1.9→42.611 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 74 117 1444
Biso mean--33.49 42.56 -
Num. residues----159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9002-2.01920.27221050.218825522657
2.0192-2.17510.26361360.202525352671
2.1751-2.3940.25131210.194525802701
2.394-2.74030.25951560.204425602716
2.7403-3.45230.24151300.188526212751
3.4523-42.6220.18431520.153227782930
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)
11.05260.67980.83961.25730.91381.15560.3632-0.32890.43740.4275-0.07590.3556-0.5899-0.1437-0.05740.5022-0.07080.26210.197-0.10630.3468-4.059329.1754-5.2113
21.52950.245-0.05841.75550.2461.01160.4678-0.57810.57920.8295-0.49360.248-0.3306-0.0922-0.02670.7878-0.33010.18310.4028-0.20150.47275.051437.01244.5552
33.07281.0523-1.09712.2669-0.03294.41050.3441-0.4043-0.0030.21910.0096-0.0739-0.3640.1929-0.28680.2617-0.07480.08920.1501-0.02670.2069-4.01519.9505-4.2361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 50 )A0 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 88 )A51 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 158 )A89 - 158

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