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- PDB-3srw: S. aureus Dihydrofolate Reductase complexed with novel 7-aryl-2,4... -

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Basic information

Entry
Database: PDB / ID: 3srw
TitleS. aureus Dihydrofolate Reductase complexed with novel 7-aryl-2,4-diaminoquinazolines
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / dihydrofolate reductase / DHFR / drug design / enzyme inhibitors / folate / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


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, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-Q27 / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsHilgers, M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Structure-based design of new DHFR-based antibacterial agents: 7-aryl-2,4-diaminoquinazolines.
Authors: Li, X. / Hilgers, M. / Cunningham, M. / Chen, Z. / Trzoss, M. / Zhang, J. / Kohnen, L. / Lam, T. / Creighton, C. / G C, K. / Nelson, K. / Kwan, B. / Stidham, M. / Brown-Driver, V. / Shaw, K.J. / Finn, J.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4353
Polymers19,3471
Non-polymers1,0882
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.287, 79.287, 107.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11X-260-

HOH

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 19347.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-Q27 / 7-(2-ethoxynaphthalen-1-yl)-6-methylquinazoline-2,4-diamine


Mass: 344.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N4O
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000, Mg acetate, MPD, ADA buffer, pH 6.2, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: Mar345 / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→68.68 Å / Num. all: 22396 / Num. obs: 22396 / % possible obs: 98.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 36.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.69-1.799.20.1574.32749629730.15791.8
1.79-1.910.50.097.83232330830.09100
1.9-2.0310.60.06610.33084029130.066100
2.03-2.1910.70.054122897627160.054100
2.19-2.410.70.04813.12694425150.048100
2.4-2.6810.80.04214.52477822990.042100
2.68-3.0910.80.04113.42192920340.041100
3.09-3.7910.60.04212.91862717560.04299.9
3.79-5.369.80.04313.61333713550.04397.1
5.36-25.958.90.04413.566907520.04490.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.56 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.89 Å
Translation2.5 Å22.89 Å

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Processing

Software
NameVersionClassificationNB
MOSFLM3.2.17data reduction
SCALA3.2.17data scaling
PHASER2.1.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→22.38 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2371 / WRfactor Rwork: 0.2093 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8634 / SU B: 3.707 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1048 / SU Rfree: 0.1028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1145 5.1 %RANDOM
Rwork0.1924 ---
obs0.1939 22343 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.42 Å2 / Biso mean: 21.331 Å2 / Biso min: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.04 Å20 Å2
2---0.07 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 74 111 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221387
X-RAY DIFFRACTIONr_angle_refined_deg1.4592.0171894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21824.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62315226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.524156
X-RAY DIFFRACTIONr_chiral_restr0.090.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021035
X-RAY DIFFRACTIONr_nbd_refined0.1940.2613
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2936
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.214
X-RAY DIFFRACTIONr_mcbond_it0.7281.5805
X-RAY DIFFRACTIONr_mcangle_it1.07621282
X-RAY DIFFRACTIONr_scbond_it1.7783702
X-RAY DIFFRACTIONr_scangle_it2.6254.5612
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 98 -
Rwork0.327 1474 -
all-1572 -
obs--96.26 %
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)
11.4516-0.3398-0.12061.19730.01791.81770.01920.03680.0844-0.07360.0032-0.00110.2121-0.0362-0.02240.0090.0139-0.0653-0.0766-0.0067-0.058-1.291-24.5498.662
20.7925-0.8186-0.12391.6460.10241.39980.14210.0508-0.1529-0.0482-0.05330.16540.3978-0.0643-0.08880.0994-0.0105-0.105-0.0764-0.0221-0.0146-5.751-33.8753.215
33.6405-2.23771.7113.1493-1.55911.26770.38220.3391-0.1786-0.8208-0.3992-0.20550.18840.22540.01710.17330.1046-0.0339-0.0302-0.0358-0.05057.556-37.6-4.416
41.4801-0.78180.35651.28720.21822.13230.11190.13120.0899-0.1749-0.0401-0.14120.22780.0046-0.07180.00930.014-0.048-0.07940.0016-0.0450.237-23.9463.092
56.4314-0.54882.94129.3271-4.87857.705-0.36610.11390.7390.0960.1179-0.2672-0.673-0.07770.24820.06030.008-0.0779-0.0770.02130.01290.888-13.1744.127
63.30860.5923-2.66622.998-2.88217.2444-0.0359-0.0171-0.09750.0020.0007-0.06020.1174-0.2180.0353-0.0476-0.0159-0.0554-0.06790.0236-0.0932-11.787-18.5673.784
70.3185-0.65420.71463.4952-1.10261.6651-0.0623-0.01460.0009-0.155-0.0381-0.11410.24140.15260.10040.08510.0551-0.0733-0.0328-0.01050.0086.825-31.5666.101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X2 - 20
2X-RAY DIFFRACTION2X21 - 57
3X-RAY DIFFRACTION3X58 - 85
4X-RAY DIFFRACTION4X86 - 123
5X-RAY DIFFRACTION5X124 - 130
6X-RAY DIFFRACTION6X131 - 158
7X-RAY DIFFRACTION7X169

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