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- PDB-5kn9: MutY N-terminal domain in complex with DNA containing an intrahel... -

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Basic information

Entry
Database: PDB / ID: 5kn9
TitleMutY N-terminal domain in complex with DNA containing an intrahelical oxoG:A base-pair
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3')
  • DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3')
KeywordsHydrolase/DNA / adenine glycosylase / oxoG / DNA repair protein / intrahelical lesion recognition / Hydrolase-DNA complex
Function / homology
Function and homology information


adenine glycosylase / adenine/guanine mispair binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / Helix-hairpin-helix motif / MutY, C-terminal / NUDIX domain / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) ...A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / Helix-hairpin-helix motif / MutY, C-terminal / NUDIX domain / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / NUDIX hydrolase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWang, L. / Chakravarthy, S. / Verdine, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA100742 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase.
Authors: Wang, L. / Chakravarthy, S. / Verdine, G.L.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenine DNA glycosylase
C: DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3')
D: DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2566
Polymers32,8253
Non-polymers4323
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-44 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.878, 38.759, 82.960
Angle α, β, γ (deg.)90.00, 105.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenine DNA glycosylase / oxoG:A-specific adenine glycosylase


Mass: 26694.490 Da / Num. of mol.: 1 / Fragment: UNP residues 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus / Gene: mutY / Production host: Escherichia coli (E. coli)
References: UniProt: P83847, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3')


Mass: 3051.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)
#3: DNA chain DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3')


Mass: 3078.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Geobacillus stearothermophilus (bacteria)

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Non-polymers , 3 types, 168 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 300 mM Ca(OAc)2, 14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.93→79.88 Å / Num. obs: 23193 / % possible obs: 99.5 % / Redundancy: 3.6 % / Net I/σ(I): 10.9
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 0.11

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRQ

1rrq


Resolution: 1.93→79.879 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.2287 1187 5.12 %
Rwork0.1687 --
obs0.1718 23171 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.93→79.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 407 10 165 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082327
X-RAY DIFFRACTIONf_angle_d1.3163251
X-RAY DIFFRACTIONf_dihedral_angle_d19.335897
X-RAY DIFFRACTIONf_chiral_restr0.043348
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9302-2.0180.30531410.22982724X-RAY DIFFRACTION100
2.018-2.12440.26661360.20752733X-RAY DIFFRACTION100
2.1244-2.25750.24471550.17712751X-RAY DIFFRACTION100
2.2575-2.43180.25781490.18032747X-RAY DIFFRACTION100
2.4318-2.67660.26761280.17492748X-RAY DIFFRACTION100
2.6766-3.06390.27051560.18232753X-RAY DIFFRACTION99
3.0639-3.86020.22531430.1472778X-RAY DIFFRACTION99
3.8602-79.94710.17881790.1512750X-RAY DIFFRACTION97
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)
16.95473.4591-2.60863.2406-4.79149.55430.16970.09570.39720.32570.110.8998-0.416-0.7928-0.24410.15960.03090.01470.2186-0.01430.287-15.38428.0023-11.0229
21.1761-0.2226-0.09182.5213-0.32916.308-0.22170.18540.181-0.68470.2116-0.1834-0.52060.2610.01690.3672-0.1331-0.020.23420.01970.1964-0.90837.039-31.378
31.4647-0.8041.10411.5432-1.70052.6819-0.08220.45990.1165-0.9675-0.0228-0.39440.15480.48580.25860.8046-0.3380.1730.58490.00780.16934.47230.3772-42.2879
47.6997-0.17556.70013.04462.0529.23370.1020.5179-0.1637-0.64050.0216-0.24410.21340.3445-0.21890.5729-0.15780.03790.3464-0.01380.16710.0147-7.1176-39.7554
55.306-1.98591.43720.8587-0.36876.1375-0.19670.3232-0.7019-0.2734-0.01090.30870.3068-0.28950.1580.4991-0.1771-0.05910.2687-0.02350.3026-10.4743-9.862-35.1166
60.81190.40221.32471.95111.42734.5096-0.0651-0.04770.0208-0.29330.05660.19220.0295-0.42520.00120.178-0.0799-0.05390.1740.03840.1805-8.1227-2.9198-19.67
74.3657-2.46410.4294.18140.48971.05470.0643-0.0036-0.38230.01530.00870.45120.4152-0.3129-0.07770.2285-0.1027-0.00820.21050.02820.1621-7.7763-9.9924-12.3505
86.15223.73782.99974.44192.41973.9162-0.13230.09350.4752-0.10330.07710.5493-0.1048-0.22460.05270.1855-0.0631-0.04310.16420.05360.2206-11.35183.9972-18.1496
94.1337-0.5724-2.09087.11761.216.5525-0.1525-0.08160.6273-0.14070.0878-0.4756-0.56110.42330.07260.2298-0.074-0.04690.12820.02620.1783-0.48448.0714-6.6452
105.7579-4.5419-1.1848.06031.38334.624-0.3183-0.3501-0.10170.74940.2535-0.16120.41540.10910.03130.2382-0.0446-0.03170.11590.02180.1362-1.8299-1.0667-2.3419
114.70993.50930.34184.079-1.40183.1553-0.19720.1328-0.1663-0.4370.0548-0.7760.22730.65230.05370.2171-0.03840.07220.323-0.07550.431511.8715-9.5652-21.9416
125.0819-0.71020.09620.1855-0.26031.09470.1415-0.5411-0.2855-0.4974-0.0682-0.99480.00320.157-0.10280.259-0.10040.01640.31770.02590.509110.1363-9.578-20.5985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 88 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 124 )
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 155 )
7X-RAY DIFFRACTION7chain 'A' and (resid 156 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 196 )
9X-RAY DIFFRACTION9chain 'A' and (resid 197 through 210 )
10X-RAY DIFFRACTION10chain 'A' and (resid 211 through 229 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 12 )
12X-RAY DIFFRACTION12chain 'D' and (resid 13 through 22 )

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