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- PDB-5uuf: Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adeni... -

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Basic information

Entry
Database: PDB / ID: 5uuf
TitleBacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (12-mer product complex)
Components
  • DNA (5'-D(*CP*CP*CP*CP*AP*(ORP)P*AP*GP*CP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*GP*CP*TP*TP*TP*GP*GP*GP*G)-3')
  • DNA-7-methylguanine glycosylase
KeywordsHYDROLASE/DNA/ANTIBIOTIC / DNA glycosylase / Protein-DNA complex / Alkylpurine / Bulky lesion / HYDROLASE-DNA-ANTIBIOTIC complex
Function / homology
Function and homology information


Leucine-rich Repeat Variant - #90 / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
yatakemycin-adenine nucleobase adduct / DNA / DNA (> 10) / DNA-7-methylguanine glycosylase / DNA alkylation repair protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.612 Å
AuthorsMullins, E.A. / Eichman, B.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517695 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES019625 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)T32 ES007028 United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Toxicity and repair of DNA adducts produced by the natural product yatakemycin.
Authors: Mullins, E.A. / Shi, R. / Eichman, B.F.
History
DepositionFeb 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,6044
Polymers35,7893
Non-polymers8151
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-17 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.173, 94.607, 48.167
Angle α, β, γ (deg.)90.000, 111.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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, UniProt: Q816E8*PLUS
#2: DNA chain DNA (5'-D(*CP*CP*CP*CP*AP*(ORP)P*AP*GP*CP*CP*CP*G)-3')


Mass: 3460.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*GP*GP*CP*TP*TP*TP*GP*GP*GP*G)-3')


Mass: 3750.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-YTA / yatakemycin-adenine nucleobase adduct


Mass: 814.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H34N10O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 19% w/v PEG4000, 42 mM sodium acetate, pH 4.6, 85 mM ammonium acetate, 5% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 41441 / % possible obs: 98.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.89 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.032 / Rrim(I) all: 0.062 / Χ2: 1.253 / Net I/σ(I): 11.5 / Num. measured all: 153245
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.61-1.673.10.4870.8670.3070.5781.07389.5
1.67-1.733.50.4290.9210.2640.5051.11198.4
1.73-1.813.70.3570.9460.2150.4181.14100
1.81-1.913.80.2570.9650.1540.31.219100
1.91-2.033.80.1820.9790.1090.2121.377100
2.03-2.193.80.1150.990.0690.1351.535100
2.19-2.43.80.0750.9950.0450.0881.367100
2.4-2.753.80.0580.9960.0340.0681.394100
2.75-3.473.80.0420.9970.0250.0491.298100
3.47-503.70.0240.9990.0150.0280.93499.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BVS

3bvs


Resolution: 1.612→36.421 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.74
RfactorNum. reflection% reflection
Rfree0.1908 2014 4.87 %
Rwork0.1536 --
obs0.1554 41372 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.93 Å2 / Biso mean: 29.1679 Å2 / Biso min: 10.61 Å2
Refinement stepCycle: final / Resolution: 1.612→36.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 477 93 314 2797
Biso mean--22.98 37.13 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012615
X-RAY DIFFRACTIONf_angle_d1.0883666
X-RAY DIFFRACTIONf_chiral_restr0.06387
X-RAY DIFFRACTIONf_plane_restr0.008377
X-RAY DIFFRACTIONf_dihedral_angle_d15.3441449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6119-1.65220.33181280.2722413254185
1.6522-1.69690.29741410.24392724286596
1.6969-1.74680.25951520.22272788294099
1.7468-1.80320.27261450.197828482993100
1.8032-1.86770.22691360.183528743010100
1.8677-1.94240.21541450.175128312976100
1.9424-2.03080.23411500.169328282978100
2.0308-2.13790.1851410.155628753016100
2.1379-2.27180.18761410.142628623003100
2.2718-2.44720.17971530.143428483001100
2.4472-2.69340.18941410.144928603001100
2.6934-3.08290.16721530.148928483001100
3.0829-3.88350.17671440.139328733017100
3.8835-36.43070.16181440.13432886303099
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)
11.05810.43080.83431.0391-0.06150.8456-0.0974-0.18370.76040.15620.04590.1192-0.7389-0.40620.01180.26390.08440.02330.16320.04790.303726.63822.739321.2247
20.53090.1106-0.2390.0843-0.01350.1476-0.1501-0.56510.07420.14540.1151-0.07650.17850.48170.00820.16850.0681-0.01160.3182-0.00580.126239.71189.615529.0359
31.00410.0971-0.38651.41180.06141.21150.06080.10230.3768-0.09660.05060.1123-0.2708-0.14460.07260.18760.06570.0010.1710.04230.183630.129517.227116.4266
40.93680.2738-0.26620.2698-0.3420.4438-0.07740.2405-0.00330.01080.15040.10530.0192-0.2516-0.0550.17280.04190.00260.26510.04190.184229.513114.20789.9769
50.7394-0.4705-0.30951.0907-0.06051.19110.07310.26570.0451-0.06190.04970.055-0.0833-0.056300.13220.01780.00680.20750.04090.146939.889212.64210.1394
60.6821-0.72020.01950.8379-0.21590.54230.07810.282-0.0577-0.0461-0.00490.12180.1349-0.1750.00060.1534-0.0014-0.01580.2279-0.01580.133341.79773.0767-1.0158
70.315-0.0546-0.17430.5734-0.31310.30490.05580.241-0.0604-0.1578-0.1091-0.07570.22290.1048-0.00020.15150.0344-0.00270.2743-0.01210.140752.41181.7962-3.3591
80.7701-0.07190.23371.2237-0.39410.8894-0.02140.1843-0.3955-0.0864-0.04230.00320.37830.0335-0.00010.20940.01680.00620.1699-0.06380.221948.6366-8.72782.0773
90.4027-0.7461-0.18541.5473-0.07861.1223-0.2379-0.3428-0.62660.26450.2327-0.21270.13770.0401-0.04670.22160.082-0.01120.22360.04250.292843.6855-6.122818.7654
100.5080.392-0.22971.9566-0.46531.119-0.3537-0.1107-0.66120.10850.11670.07140.071-0.053-0.00290.22750.0120.01150.25590.03780.30741.5833-5.842117.602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )A1 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 27 )A16 - 27
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 73 )A28 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 90 )A74 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 143 )A91 - 143
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 162 )A144 - 162
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 178 )A163 - 178
8X-RAY DIFFRACTION8chain 'A' and (resid 179 through 226 )A179 - 226
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 12 )B1 - 12
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 12 )C1 - 12

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