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- PDB-3sr5: S. aureus Dihydrofolate Reductase complexed with novel 7-aryl-2,4... -

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Basic information

Entry
Database: PDB / ID: 3sr5
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-Q12 / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 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 6, 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)20,2703
Polymers19,2161
Non-polymers1,0542
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.173, 79.173, 107.235
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: 19215.891 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-Q12 / 7-(3,4-dimethoxyphenyl)-6-methylquinazoline-2,4-diamine


Mass: 310.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 51.28 %
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
ReflectionRedundancy: 11.6 % / Av σ(I) over netI: 9.2 / Number: 262172 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / D res high: 1.683 Å / D res low: 68.566 Å / Num. obs: 22628 / % possible obs: 97.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.3117.9292.310.0390.0399.3
3.765.3199.410.0330.03311.1
3.073.7610010.0390.03911.9
2.663.0710010.0410.04112.1
2.382.6610010.0480.04812
2.172.3810010.0590.05912
2.012.1799.910.0780.07812
1.882.0199.710.1150.11511.9
1.771.8899.410.1760.17611.9
1.681.7785.310.2980.29810
ReflectionResolution: 1.68→68.566 Å / Num. all: 22628 / Num. obs: 22628 / % possible obs: 97.4 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 33.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.68-1.77100.2982.52818328070.29885.3
1.77-1.8811.90.1764.23705031240.17699.4
1.88-2.0111.90.1156.33507429400.11599.7
2.01-2.17120.0788.63306527650.07899.9
2.17-2.38120.05911.33096425750.059100
2.38-2.66120.04813.22820423410.048100
2.66-3.0712.10.04113.82520720880.041100
3.07-3.7611.90.03913.42141017920.039100
3.76-5.3111.10.03317.61577914220.03399.4
5.31-17.9239.30.03915.172367740.03992.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å17.32 Å
Translation2.5 Å17.32 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.17data scaling
PHASER1.3.2phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→17.14 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.438 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 1155 5.1 %RANDOM
Rwork0.1945 ---
obs0.1961 22597 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.29 Å2 / Biso mean: 21.955 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.68→17.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 71 118 1461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221383
X-RAY DIFFRACTIONr_angle_refined_deg1.4322.0141888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92624.19462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31615226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.812156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021032
X-RAY DIFFRACTIONr_nbd_refined0.1910.2606
X-RAY DIFFRACTIONr_nbtor_refined0.310.2937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.215
X-RAY DIFFRACTIONr_mcbond_it0.6941.5805
X-RAY DIFFRACTIONr_mcangle_it1.0521282
X-RAY DIFFRACTIONr_scbond_it1.8443687
X-RAY DIFFRACTIONr_scangle_it2.7074.5606
LS refinement shellResolution: 1.683→1.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 73 -
Rwork0.44 1197 -
all-1270 -
obs--77.72 %
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)
11.48350.33790.36531.16320.20612.97180.0408-0.01310.09280.0567-0.04510.020.20990.04060.0043-0.0149-0.0106-0.0551-0.06180.0054-0.06411.333-24.516-8.608
20.91591.0809-0.12352.1564-0.16141.14660.141-0.0264-0.2007-0.0285-0.0704-0.17060.37470.0663-0.07060.06650.0195-0.1014-0.06730.0167-0.02825.803-33.846-3.171
33.78613.16051.22484.22081.06880.93190.4452-0.3414-0.22360.7383-0.43510.36060.2076-0.1439-0.010.1222-0.113-0.0343-0.02240.0375-0.0439-7.504-37.5964.458
41.4140.69130.61011.13760.02581.67710.1136-0.12320.09190.1325-0.04370.11710.1911-0.0429-0.07-0.0098-0.0168-0.0414-0.06110.0022-0.0645-0.197-23.922-3.034
57.47011.7464.0338.54033.26438.8341-0.3016-0.15170.73180.07580.02380.4225-0.67260.12920.27780.059-0.0044-0.0559-0.0594-0.0218-0.0183-0.858-13.147-4.055
64.0829-0.7908-3.06693.31022.91846.6772-0.0165-0.0024-0.104-0.03250.0589-0.03340.06410.2353-0.0423-0.0524-0.0013-0.0503-0.0593-0.025-0.10111.825-18.528-3.718
70.1030.11680.43133.18571.42632.0937-0.0834-0.0043-0.0214-0.0142-0.03350.2870.2316-0.21570.11690.0763-0.052-0.0972-0.01720.02120.0299-6.778-31.546-6.056
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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