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- PDB-7lxh: Bacillus cereus DNA glycosylase AlkD bound to a CC1065-adenine nu... -

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Basic information

Entry
Database: PDB / ID: 7lxh
TitleBacillus cereus DNA glycosylase AlkD bound to a CC1065-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-YNG / DNA / DNA-7-methylguanine glycosylase
Function and homology information
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.667 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)34,8526
Polymers33,9333
Non-polymers9193
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-27 kcal/mol
Surface area13600 Å2
Unit cell
Length a, b, c (Å)124.572, 55.609, 48.557
Angle α, β, γ (deg.)90.000, 110.730, 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, 360 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 838.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H38N12O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% (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-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.667→50 Å / Num. obs: 35848 / % possible obs: 98.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Χ2: 1.203 / Net I/av σ(I): 25.5 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.67-1.74.90.4616400.8930.220.5120.9391.9
1.7-1.735.40.47317380.8820.2150.5210.95296.8
1.73-1.7660.44417920.9220.1930.4850.96699.1
1.76-1.86.20.38318490.9370.1650.4181.00899.9
1.8-1.846.40.34317740.9550.1460.3741.05499.9
1.84-1.886.60.32217790.960.1360.351.112100
1.88-1.936.40.28518010.9580.1220.311.3100
1.93-1.986.60.23918050.9750.1010.261.187100
1.98-2.046.60.18118070.9860.0760.1971.141100
2.04-2.16.60.15318050.9890.0640.1671.284100
2.1-2.186.60.13218230.9910.0550.1431.423100
2.18-2.276.30.12617940.9890.0540.1371.50799.7
2.27-2.376.20.10117980.9930.0430.111.45299.2
2.37-2.496.60.08318180.9950.0350.091.496100
2.49-2.656.60.06718320.9970.0280.0731.36100
2.65-2.866.60.06118070.9970.0250.0661.318100
2.86-3.146.60.06118100.9970.0250.0661.269100
3.14-3.66.30.04818010.9980.020.0521.11898.2
3.6-4.535.80.03117010.9990.0130.0330.91292.2
4.53-506.40.02918740.9990.0120.0311.03799.4

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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: 1.667→31.84 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1828 1793 5 %RANDOM
Rwork0.1487 34050 --
obs0.1504 35843 98.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.15 Å2 / Biso mean: 31.893 Å2 / Biso min: 11.35 Å2
Refinement stepCycle: final / Resolution: 1.667→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 354 102 357 2736
Biso mean--23.25 36.32 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012456
X-RAY DIFFRACTIONf_angle_d1.0673419
X-RAY DIFFRACTIONf_dihedral_angle_d16.7321378
X-RAY DIFFRACTIONf_chiral_restr0.059358
X-RAY DIFFRACTIONf_plane_restr0.008364
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.667-1.7120.26461180.2187237890
1.712-1.76240.23041400.1988259899
1.7624-1.81930.20651450.17782618100
1.8193-1.88430.22131380.16912686100
1.8843-1.95970.23751360.18892625100
1.9597-2.04890.20361400.16562641100
2.0489-2.15690.21631420.162633100
2.1569-2.2920.18361390.1512264499
2.292-2.46890.17981400.14172640100
2.4689-2.71730.17631410.13942673100
2.7173-3.11020.15321400.13932675100
3.1102-3.91740.17081300.13254795
3.9174-31.840.16571440.1381269298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.92181.91842.53114.44270.21443.8768-0.0874-0.7245-0.10920.5999-0.0804-0.3691-0.15070.1359-0.02270.30940.0675-0.09580.6749-0.00560.2096-18.6867-5.156337.6725
22.21470.1585-0.28192.43860.83533.7651-0.0894-0.7016-0.0380.2583-0.0986-0.07310.10950.03420.14170.19820.0509-0.0010.40080.04690.1868-28.5068-10.44130.3262
33.93440.2701-0.04487.81323.17912.9523-0.2636-0.87090.4980.05230.2487-0.3659-0.73410.7692-0.1010.4016-0.0989-0.10.5165-0.08170.2414-16.35352.083229.3899
44.21710.8569-0.33487.34570.75921.15020.0421-0.67880.47810.13930.01360.1951-0.70840.0973-0.01980.44280.0356-0.01820.3466-0.10190.1924-24.26222.357226.5162
53.27481.4045-0.08874.7807-1.04661.6263-0.0193-0.25880.19540.343-0.0463-0.1035-0.22240.18650.0650.22160.0137-0.03080.1908-0.02660.1311-20.55440.865116.5927
62.2347-0.93110.11072.7016-1.01521.4439-0.0513-0.16240.21650.15510.0381-0.1141-0.0870.082-0.00220.1541-0.0056-0.01170.1006-0.02020.1338-23.41145.84117.3301
71.6945-1.0764-0.17872.95550.21331.18990.02640.0753-0.0889-0.1174-0.05130.14390.0254-0.08320.01590.1669-0.012-0.00170.1068-0.00680.1555-34.6509-1.7213-1.7375
83.53390.3241-0.34763.08240.20334.2707-0.1486-0.1705-0.10640.4559-0.02840.24770.1978-0.35880.16260.2067-0.01770.0510.1704-0.00160.148-41.8222-7.992716.2361
91.79920.08370.3544.17534.00656.4626-0.0446-0.1771-0.06220.1675-0.24240.27230.1012-0.17150.29380.22760.00960.02510.22650.02120.2085-41.6076-11.140516.8095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )A-1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 53 )A16 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 73 )A54 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 90 )A74 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 118 )A91 - 118
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 162 )A119 - 162
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 225 )A163 - 225
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 9 )B1 - 9
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 9 )C1 - 9

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