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- PDB-7lxj: Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-ad... -

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Basic information

Entry
Database: PDB / ID: 7lxj
TitleBacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-adenine nucleobase adduct and DNA containing an abasic site
Components
  • DNA (5'-D(*AP*GP*CP*AP*AP*(ORP)P*GP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*CP*TP*TP*TP*GP*C)-3')
  • DNA-7-methylguanine glycosylase
KeywordsHYDROLASE/DNA/ANTIBIOTIC / DNA Repair / Base Excision Repair / Antibiotic Self-Resistance / Bulky DNA Adduct / Secondary Metabolite / DNA BINDING PROTEIN / HYDROLASE-DNA-ANTIBIOTIC complex
Function / homologyDNA alkylation repair enzyme / DNA alkylation repair enzyme / Armadillo-type fold / Chem-YNY / DNA / DNA-7-methylguanine glycosylase
Function and homology information
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMullins, E.A. / Eichman, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1928918 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites.
Authors: Mullins, E.A. / Dorival, J. / Tang, G.L. / Boger, D.L. / Eichman, B.F.
History
DepositionMar 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: DNA-7-methylguanine glycosylase
B: DNA (5'-D(*AP*GP*CP*AP*AP*(ORP)P*GP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*CP*TP*TP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6256
Polymers33,9333
Non-polymers6933
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-36 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.715, 55.661, 47.991
Angle α, β, γ (deg.)90.000, 112.200, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA-7-methylguanine glycosylase / AlkD


Mass: 28578.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: bcere0015_46090 / Plasmid: PBG103 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: C2T7T7

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*GP*CP*AP*AP*(ORP)P*GP*GP*C)-3')


Mass: 2656.739 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*CP*CP*TP*TP*TP*GP*C)-3')


Mass: 2697.771 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 192 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-YNY / methyl (8R)-8-{[(4P)-6-amino-3H-purin-3-yl]methyl}-4-hydroxy-6-(5,6,7-trimethoxy-1H-indole-2-carbonyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indole-2-carboxylate


Mass: 612.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28N8O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 24% (w/v) PEG 8000, 50 mM HEPES pH 7.0, and 50 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 8, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 22584 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 1.061 / Net I/av σ(I): 24.7 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-2.015.90.59822100.8360.2590.6540.81298.8
2.01-2.096.20.44722570.9180.1920.4880.89100
2.09-2.186.30.30322300.9560.1290.330.977100
2.18-2.36.30.21722660.9750.0920.2361.09100
2.3-2.446.40.16122460.9860.0690.1761.031100
2.44-2.636.40.12222650.990.0520.1331.065100
2.63-2.96.40.08922380.9950.0370.0961.028100
2.9-3.326.40.06322540.9970.0260.0691.215100
3.32-4.186.30.04322860.9990.0180.0471.4100
4.18-506.20.0323320.9990.0130.0331.06399.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
PHENIXphasing
PHASERphasing
Cootmodel building
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BVS

3bvs


Resolution: 1.93→44.434 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 1132 5.01 %RANDOM
Rwork0.1539 21443 --
obs0.1564 22575 97.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.88 Å2 / Biso mean: 45.5047 Å2 / Biso min: 17.29 Å2
Refinement stepCycle: final / Resolution: 1.93→44.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 354 75 189 2541
Biso mean--57.58 41.71 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112435
X-RAY DIFFRACTIONf_angle_d1.1163383
X-RAY DIFFRACTIONf_dihedral_angle_d20.811922
X-RAY DIFFRACTIONf_chiral_restr0.059358
X-RAY DIFFRACTIONf_plane_restr0.008362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9302-2.01810.28971180.236229084
2.0181-2.12450.25521460.19392692100
2.1245-2.25760.2031420.16462721100
2.2576-2.43190.20291470.15382737100
2.4319-2.67660.23841430.16012722100
2.6766-3.06380.20141410.15782733100
3.0638-3.85970.18681490.14372754100
3.8597-44.4340.18211460.14032794100

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