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- PDB-3m09: F98Y TMP-resistant Dihydrofolate Reductase from Staphylococcus au... -

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Basic information

Entry
Database: PDB / ID: 3m09
TitleF98Y TMP-resistant Dihydrofolate Reductase from Staphylococcus aureus with inhibitor RAB1
ComponentsDihydrofolate reductase
KeywordsOxidoreductase/Oxidoreductase Inhibitor / folate / dhfr / antimicrobial / antibiotic resistance / NADP / One-carbon metabolism / Oxidoreductase / Oxidoreductase-Oxidoreductase Inhibitor complex
Function / homology
Function and homology information


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-RAR / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.009 Å
AuthorsBourne, C.R. / Barrow, W.W.
Citation
Journal: Antimicrob.Agents Chemother. / Year: 2010
Title: Inhibition of Antibiotic-Resistant Staphylococcus aureus by the Broad-Spectrum Dihydrofolate Reductase Inhibitor RAB1.
Authors: Bourne, C.R. / Barrow, E.W. / Bunce, R.A. / Bourne, P.C. / Berlin, K.D. / Barrow, W.W.
#1: Journal: Antimicrob.agents chemother. / Year: 2009
Title: Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity
Authors: Bourne, C.R. / Bunce, R.A. / Bourne, P.C. / Berlin, K.D. / Barrow, E.W. / Barrow, W.W.
History
DepositionMar 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 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)19,7784
Polymers18,4561
Non-polymers1,3223
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.180, 79.180, 107.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 18456.076 Da / Num. of mol.: 1 / Mutation: F98Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Plasmid: pET101d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-RAR / 5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1-propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine-2,4-diamine / (S)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)-2,3-dimethoxyphenyl)-1-(1-propylphthalazin-2(1H)-yl)prop-2-en-1-one


Mass: 486.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30N6O3
#3: 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 298 K / Method: sitting drop / pH: 6.5
Details: 15% PEG 6000, 0.15 M sodium acetate, 0.1M MES buffer, pH 6.5, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.009→42.395 Å / Num. all: 13953 / Num. obs: 13953 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.093 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.01-2.127.20.4031.61424919830.403100
2.12-2.257.40.2852.31388818660.285100
2.25-2.47.50.2292.61327717820.229100
2.4-2.597.50.1743.71236116480.174100
2.59-2.847.50.134.91153915480.13100
2.84-3.187.50.0847.61046714020.084100
3.18-3.677.40.05611.3920312420.056100
3.67-4.497.30.0415.7787110800.04100
4.49-6.357.10.0361761298660.036100
6.35-42.46.20.03415.333275360.03499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.59 Å
Translation2.5 Å39.59 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASER2.1.1phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.009→39.59 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.26 / σ(F): 0.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 2539 10.07 %
Rwork0.169 --
obs0.173 13904 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.036 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 62.67 Å2 / Biso mean: 20.142 Å2 / Biso min: 3.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.031 Å20 Å20 Å2
2---0.031 Å2-0 Å2
3---0.063 Å2
Refinement stepCycle: LAST / Resolution: 2.009→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1291 0 90 166 1547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051445
X-RAY DIFFRACTIONf_angle_d1.0181976
X-RAY DIFFRACTIONf_chiral_restr0.082218
X-RAY DIFFRACTIONf_plane_restr0.007241
X-RAY DIFFRACTIONf_dihedral_angle_d28.308593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.009-2.0810.2312580.18822742532
2.081-2.1640.2432510.17522672518
2.164-2.2630.2242540.17122832537
2.263-2.3820.2252580.16922562514
2.382-2.5310.2082550.17322642519
2.531-2.7270.2452510.17322732524
2.727-3.0010.2292450.16722632508
3.001-3.4350.1812590.16322812540
3.435-4.3270.152530.13822552508
4.327-39.5980.1772550.16322712526
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)
10.2382-0.1057-0.08230.05080.06120.8678-0.00130.023-0.0937-0.0514-0.00790.08570.2980.0055-0.02430.11350.0035-0.0470.0269-0.00210.0672-4.0443-29.76735.8051
21.0462-0.69380.34020.4669-0.26770.41680.2610.2041-0.2584-0.3884-0.12390.06410.28730.1083-0.08710.23730.0523-0.03230.082-0.01610.1434.6475-36.7159-4.5829
30.4132-0.07050.17640.2503-0.04350.5408-0.01970.03590.0737-0.01720.0458-0.07320.1028-0.0017-0.01610.0535-0.0067-0.02050.01620.01140.0484-3.9105-18.85673.7194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:51)A1 - 51
2X-RAY DIFFRACTION2(chain A and resid 52:90)A52 - 90
3X-RAY DIFFRACTION3(chain A and resid 91:161)A91 - 161

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