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

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Basic information

Entry
Database: PDB / ID: 5uug
TitleBacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (9-mer product complex)
Components
  • DNA (5'-D(*AP*GP*GP*CP*AP*(ORP)P*AP*GP*C)-3')
  • DNA (5'-D(*TP*GP*CP*TP*TP*TP*GP*CP*C)-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-7-methylguanine glycosylase / DNA alkylation repair protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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*GP*CP*AP*(ORP)P*AP*GP*C)-3')
C: DNA (5'-D(*TP*GP*CP*TP*TP*TP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7875
Polymers33,9333
Non-polymers8552
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26 kcal/mol
Surface area13250 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, UniProt: Q816E8*PLUS

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*GP*GP*CP*AP*(ORP)P*AP*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*TP*TP*TP*GP*CP*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, 393 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-YTA / yatakemycin-adenine nucleobase adduct


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


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG8000, 50 mM HEPES, pH 7.0, 50 mM calcium chloride

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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: 1.71→50 Å / Num. obs: 32871 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.89 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Χ2: 1.218 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.71-1.775.90.5770.8770.2590.6341.052100
1.77-1.846.20.470.920.2050.5141.141100
1.84-1.936.40.3740.9540.160.4071.232100
1.93-2.036.50.2920.970.1240.3181.385100
2.03-2.156.60.2140.9840.090.2331.53100
2.15-2.326.60.1550.990.0650.1691.48100
2.32-2.556.70.1140.9940.0480.1241.355100
2.55-2.926.70.0820.9960.0340.0891.258100
2.92-3.686.60.0540.9980.0230.0581.089100
3.68-506.50.0340.9990.0150.0370.63399.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BVS

3bvs


Resolution: 1.712→44.434 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6
RfactorNum. reflection% reflection
Rfree0.1769 1646 5.01 %
Rwork0.1362 --
obs0.1383 32863 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.16 Å2 / Biso mean: 27.6548 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: final / Resolution: 1.712→44.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 354 94 391 2762
Biso mean--28.52 36.95 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012462
X-RAY DIFFRACTIONf_angle_d1.3133426
X-RAY DIFFRACTIONf_chiral_restr0.054359
X-RAY DIFFRACTIONf_plane_restr0.008367
X-RAY DIFFRACTIONf_dihedral_angle_d18.102920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.712-1.76240.23381340.19622531266599
1.7624-1.81920.22811290.170525782707100
1.8192-1.88430.20681410.163826122753100
1.8843-1.95970.20241340.159425802714100
1.9597-2.04890.18041400.150825952735100
2.0489-2.15690.16181350.139225902725100
2.1569-2.29210.17781390.127326122751100
2.2921-2.4690.20341380.127425912729100
2.469-2.71740.18511380.132426132751100
2.7174-3.11060.1361360.131726222758100
3.1106-3.91860.17251410.12226112752100
3.9186-44.44870.17021410.131226822823100
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)
13.97432.1150.72195.8170.35721.41140.0105-0.4659-0.19720.355-0.1275-0.56390.16530.40770.15550.24220.0571-0.0440.41110.02890.2385-19.2604-4.558137.7049
28.2836-0.79783.58172.9503-0.72254.27130.0177-0.5542-0.48590.2929-0.20350.15821.0861-0.43440.12980.3255-0.01030.03580.21520.04030.173-30.8147-18.242128.1645
31.85130.069-0.43493.70721.24262.1795-0.013-0.18350.12280.12260.0082-0.2176-0.00390.31970.01790.14860.0548-0.03320.26890.02610.1205-23.1797-2.728330.4605
41.6852.6126-1.40784.9213-1.92853.66530.0798-0.13610.11870.30640.03710.1593-0.24220.1165-0.08480.13210.0342-0.02720.2423-0.02240.1513-20.43413.836422.0094
50.9679-0.44790.01691.444-0.11130.9591-0.021-0.03980.0221-0.06530.01350.02650.00450.04810.01270.1281-0.0005-0.00050.11230.00060.1083-27.30141.48184.9975
62.8445-0.518-0.55973.0934-0.00622.45140.03630.1538-0.0835-0.2307-0.10930.472-0.0405-0.31230.0480.2102-0.0033-0.0470.1759-0.03290.2362-40.114-5.1626-3.7027
75.3846-0.2907-0.4144.88461.46695.2724-0.1375-0.09730.06130.57270.01740.48710.053-0.76560.15470.2059-0.01130.04610.25570.00280.1788-41.436-8.046715.5166
82.56971.20870.96084.31693.68815.76850.1404-0.2699-0.06450.3021-0.31590.08220.1115-0.54370.24650.19270.01670.01990.19360.00530.1377-41.4-11.210616.5113
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 27 )A16 - 27
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 73 )A28 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 104 )A74 - 104
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 204 )A105 - 204
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 225 )A205 - 225
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 9 )B1 - 9
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 9 )C1 - 9

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