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- PDB-4q6a: Staphylococcus aureus V31L, F98Y Mutant Dihydrofolate Reductase C... -

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Basic information

Entry
Database: PDB / ID: 4q6a
TitleStaphylococcus aureus V31L, F98Y Mutant Dihydrofolate Reductase Complexed with NADPH
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesStaphylococcus aureus MUF168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsReeve, S.M. / Anderson, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Protein design algorithms predict viable resistance to an experimental antifolate.
Authors: Reeve, S.M. / Gainza, P. / Frey, K.M. / Georgiev, I. / Donald, B.R. / Anderson, A.C.
History
DepositionApr 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3144
Polymers18,4191
Non-polymers8953
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)79.331, 79.331, 107.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Dihydrofolate reductase


Mass: 18419.053 Da / Num. of mol.: 1 / Mutation: V31L, F98Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus MUF168 (bacteria)
Strain: SAB1281c / Gene: dfrB, Y000_11620 / Plasmid: pET-41a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W7NDF6, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, pH 6.0, 13% PEG 10,000, 0.3M Sodium Acetate, 5% gamma-butyrolacetone, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2013
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.099→34.351 Å / Num. all: 12235 / Num. obs: 11649 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 19.57 Å2 / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 20 / % possible all: 0.993

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3F0U

3f0u


Resolution: 2.099→34.351 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 586 4.79 %Random
Rwork0.1647 ---
obs0.1668 11649 99.87 %-
all-12235 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→34.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 58 133 1465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081418
X-RAY DIFFRACTIONf_angle_d1.21942
X-RAY DIFFRACTIONf_dihedral_angle_d13.972535
X-RAY DIFFRACTIONf_chiral_restr0.081216
X-RAY DIFFRACTIONf_plane_restr0.005245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.0992-2.31040.21961500.160828242824
2.3104-2.64460.24261400.172628622862
2.6446-3.33150.22431420.172828892889
3.3315-34.35590.18081540.158730743074

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