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- PDB-3sgy: Staphylococcus aureus Dihydrofolate Reductase complexed with NADP... -

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Basic information

Entry
Database: PDB / ID: 3sgy
TitleStaphylococcus aureus Dihydrofolate Reductase complexed with NADPH and 6-ETHYL-5-[(3S)-3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP1006)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / oxidoreductase / NADP / NADPH / One-carbon metabolism / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / 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-06W / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsFrey, K.M. / Anderson, A.C.
CitationJournal: Plos One / Year: 2012
Title: Toward New Therapeutics for Skin and Soft Tissue Infections: Propargyl-Linked Antifolates Are Potent Inhibitors of MRSA and Streptococcus pyogenes.
Authors: Viswanathan, K. / Frey, K.M. / Scocchera, E.W. / Martin, B.D. / Swain Iii, P.W. / Alverson, J.B. / Priestley, N.D. / Anderson, A.C. / Wright, D.L.
History
DepositionJun 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Non-polymer description
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9646
Polymers38,7262
Non-polymers2,2384
Water724
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4823
Polymers19,3631
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4823
Polymers19,3631
Non-polymers1,1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.826, 78.826, 107.277
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 2 / Auth seq-ID: 1 - 157 / Label seq-ID: 1 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 19363.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dfrA, dfrB, folA / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-06W / 6-ethyl-5-{(3S)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine


Mass: 373.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15 % PEG 10000, 150 mM sodium acetate, 100 mM MES pH 6.5, 5 % butyrlactone, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2010
RadiationMonochromator: Double silicon(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.598→42.18 Å / Num. all: 11695 / Num. obs: 11379 / % possible obs: 97.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.7 % / Biso Wilson estimate: 51.704 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 31.1
Reflection shellResolution: 2.598→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.5 / Num. unique all: 544 / Rsym value: 0.291 / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Sa DHFR bound to Folate and NADPH (Dale et al. 1997)

Resolution: 2.598→42.18 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.572 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.706 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 544 4.8 %RANDOM
Rwork0.214 ---
all0.2165 10835 --
obs0.2165 11379 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.3 Å2 / Biso mean: 51.7039 Å2 / Biso min: 34.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.598→42.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 152 4 2700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222776
X-RAY DIFFRACTIONr_angle_refined_deg1.2462.0173786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3224.194124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03215452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7391512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022074
X-RAY DIFFRACTIONr_nbd_refined0.1920.21183
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2104
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.25
X-RAY DIFFRACTIONr_mcbond_it0.4971.51591
X-RAY DIFFRACTIONr_mcangle_it0.90822564
X-RAY DIFFRACTIONr_scbond_it1.08831360
X-RAY DIFFRACTIONr_scangle_it1.74.51222
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
628TIGHT POSITIONAL0.010.05
645MEDIUM POSITIONAL0.330.5
628TIGHT THERMAL0.020.5
645MEDIUM THERMAL0.192
LS refinement shellResolution: 2.598→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 41 -
Rwork0.297 819 -
all-860 -
obs-548 98.74 %

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