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- PDB-3i8a: Staphylococcus aureus H30N, F98Y Dihydrofolate Reductase complexe... -

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Basic information

Entry
Database: PDB / ID: 3i8a
TitleStaphylococcus aureus H30N, F98Y Dihydrofolate Reductase complexed with NADPH and 2,4-diamino-5-(3-(2,5-dimethoxyphenyl)prop-1-ynyl)-6-ethylpyrimidine (UCP120B)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NADPH / One-carbon metabolism / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic 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, 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-N22 / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier Methods / Resolution: 2.41 Å
AuthorsFrey, K.M. / Lombardo, M.N. / Anderson, A.C.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Towards the understanding of resistance mechanisms in clinically isolated trimethoprim-resistant, methicillin-resistant Staphylococcus aureus dihydrofolate reductase.
Authors: Frey, K.M. / Lombardo, M.N. / Wright, D.L. / Anderson, A.C.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0653
Polymers18,0081
Non-polymers1,0582
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.164, 79.164, 108.960
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-181-

HOH

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Components

#1: Protein Dihydrofolate reductase / DHFR


Mass: 18007.512 Da / Num. of mol.: 1 / Mutation: H30N, H30N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dfrB, folA / Plasmid: pET41 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A017, dihydrofolate reductase
#2: Chemical ChemComp-N22 / 5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine


Mass: 312.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O2
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 10,000, 150 mM sodium acetate, 100 mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.41→37.22 Å / Num. all: 7504 / Num. obs: 7504 / % possible obs: 95.01 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 10.4 % / Biso Wilson estimate: 15.689 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 1.1
Reflection shellResolution: 2.41→2.472 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 0.8 / Num. unique all: 560 / Rsym value: 0.074 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: Difference Fourier Methods
Starting model: 3FQO

3fqo


Resolution: 2.41→37.22 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.865 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.567 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 363 4.6 %RANDOM
Rwork0.206 ---
all0.208 7504 --
obs0.208 7504 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 40.31 Å2 / Biso mean: 15.662 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.41→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 71 43 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221380
X-RAY DIFFRACTIONr_angle_refined_deg1.642.0161882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5855156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06324.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58615226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.893156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021029
X-RAY DIFFRACTIONr_nbd_refined0.2110.2577
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2907
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.24
X-RAY DIFFRACTIONr_mcbond_it0.7531.5811
X-RAY DIFFRACTIONr_mcangle_it1.31421282
X-RAY DIFFRACTIONr_scbond_it1.7773673
X-RAY DIFFRACTIONr_scangle_it2.7094.5600
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 26 -
Rwork0.237 560 -
all-586 -
obs-7504 100 %

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