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

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Basic information

Entry
Database: PDB / ID: 3sru
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 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-Q26 / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / 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)20,5403
Polymers19,3471
Non-polymers1,1932
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.105, 79.105, 107.095
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: 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-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-Q26 / N-[3'-(2,4-diaminoquinazolin-7-yl)-4'-ethoxybiphenyl-3-yl]methanesulfonamide


Mass: 449.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23N5O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
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: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→68.519 Å / Num. all: 22282 / Num. obs: 22282 / % possible obs: 98.5 % / Redundancy: 17.2 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 50.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7915.50.1424.94514729180.14290.8
1.79-1.917.40.0868.35326730570.08699.9
1.9-2.0317.50.063115070328900.063100
2.03-2.1917.60.05112.74747526940.051100
2.19-2.417.70.046144446325050.046100
2.4-2.6817.80.03915.44033722650.039100
2.68-3.117.80.03914.53632020360.039100
3.1-3.7917.70.04133089317460.04100
3.79-5.3616.80.03814.22304913730.03899.4
5.36-26.514.80.0414.5118087980.0495.7

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Processing

Software
NameVersionClassificationNB
MOSFLM3.2.17data reduction
SCALA3.2.17data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→21.1 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2191 / WRfactor Rwork: 0.1969 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8832 / SU B: 2.998 / SU ML: 0.053 / SU R Cruickshank DPI: 0.1004 / SU Rfree: 0.0944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 1136 5.1 %RANDOM
Rwork0.1816 ---
obs0.1827 22238 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.62 Å2 / Biso mean: 18.3 Å2 / Biso min: 6.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 80 133 1485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221393
X-RAY DIFFRACTIONr_angle_refined_deg1.4422.0221903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06424.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16815226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.45156
X-RAY DIFFRACTIONr_chiral_restr0.0960.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021039
X-RAY DIFFRACTIONr_nbd_refined0.1880.2604
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.216
X-RAY DIFFRACTIONr_mcbond_it0.6941.5802
X-RAY DIFFRACTIONr_mcangle_it1.0921282
X-RAY DIFFRACTIONr_scbond_it1.8153690
X-RAY DIFFRACTIONr_scangle_it2.8494.5621
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 88 -
Rwork0.264 1451 -
all-1539 -
obs--96.49 %
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)
11.3240.1193-0.12811.12320.25232.52210.0008-0.0221-0.05590.0261-0.0576-0.025-0.0954-0.03080.0568-0.0121-0.01460.0436-0.0502-0.0092-0.0508-1.26924.473-8.637
20.80710.7668-0.05321.73280.22121.74680.1278-0.040.1339-0.0105-0.07070.1549-0.306-0.0993-0.05710.03180.01380.0815-0.0654-0.021-0.0175-5.69133.803-3.156
34.29171.374-1.58022.7052-0.66651.0570.3785-0.30480.22240.5447-0.3207-0.2984-0.22570.1629-0.05770.0793-0.08650.0202-0.0359-0.0359-0.0377.63837.464.481
41.39370.755-0.33621.21880.18311.74260.0715-0.0913-0.06760.1032-0.0426-0.1127-0.1310.0122-0.0289-0.0199-0.00860.029-0.05410.0008-0.04640.26123.848-3.065
55.65281.5587-2.48699.447-4.13536.5599-0.3118-0.106-0.60530.02970.0622-0.24620.6733-0.15430.24960.0656-0.0090.0564-0.04520.0133-0.00390.87113.072-4.131
64.0074-0.87652.93062.9251-2.50356.3989-0.0585-0.06250.1255-0.05920.0056-0.0317-0.0218-0.25850.0529-0.0367-0.00390.0336-0.05290.0153-0.0803-11.78418.512-3.762
71.92282.66160.34073.76260.01622.7039-0.12630.03970.0896-0.1068-0.0416-0.2055-0.27140.1950.1680.048-0.04350.0725-0.0168-0.01220.03446.87531.456-6.061
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 DIFFRACTION7X168

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