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- PDB-2qk8: Crystal structure of the anthrax drug target, Bacillus anthracis ... -

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Basic information

Entry
Database: PDB / ID: 2qk8
TitleCrystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Methotrexate / Pteridine binding / Nucleotide phosphate binding / Pseudo-Rossman fold
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion 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
METHOTREXATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBennett, B.C. / Xu, H. / Simmerman, R.F. / Lee, R.E. / Dealwis, C.G.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase.
Authors: Bennett, B.C. / Xu, H. / Simmerman, R.F. / Lee, R.E. / Dealwis, C.G.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,6032
Polymers19,1491
Non-polymers4541
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.697, 41.236, 67.032
Angle α, β, γ (deg.)90.00, 119.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-224-

HOH

31A-230-

HOH

DetailsOnly one molecule in the asymmetric unit. Enzyme is functional as a monomer.

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Components

#1: Protein Dihydrofolate reductase /


Mass: 19148.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Sterne / Gene: dfrA / Plasmid: Champion pET-SUMO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81R22, dihydrofolate reductase
#2: Chemical ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 0.2 M CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2006
Details: Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→58.4 Å / Num. all: 16860 / Num. obs: 10104 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.099 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.342 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
BioCARSspecific programdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1ZDR (Bacillus stearothermophilus DHFR)

1zdr


Resolution: 2.4→22 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.98 / SU ML: 0.263 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2.8 / ESU R: 0.595 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27382 374 5 %RANDOM
Rwork0.24273 ---
obs0.24422 7171 95.68 %-
all-7545 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.402 Å2
Refinement stepCycle: LAST / Resolution: 2.4→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 33 48 1428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221419
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.961920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.675161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16224.24773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.54315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.184157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021101
X-RAY DIFFRACTIONr_nbd_refined0.2810.2650
X-RAY DIFFRACTIONr_nbtor_refined0.3350.2901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.27
X-RAY DIFFRACTIONr_mcbond_it0.9591.5842
X-RAY DIFFRACTIONr_mcangle_it1.72521322
X-RAY DIFFRACTIONr_scbond_it2.1673688
X-RAY DIFFRACTIONr_scangle_it3.1554.5598
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 37 -
Rwork0.366 474 -
obs-474 89.96 %

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