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- PDB-5kn8: MutY N-terminal domain in complex with undamaged DNA -

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Basic information

Entry
Database: PDB / ID: 5kn8
TitleMutY N-terminal domain in complex with undamaged DNA
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*TP*GP*TP*GP*CP*T)-3')
KeywordsHydrolase/DNA / adenine glycosylase / oxoG / DNA repair protein / lesion-scanning complex / 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: 1.81 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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*TP*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)33,1115
Polymers32,7193
Non-polymers3922
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-47 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.200, 38.618, 83.796
Angle α, β, γ (deg.)90.00, 104.00, 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: 26630.447 Da / Num. of mol.: 1 / Fragment: UNP residues 1-229 / Mutation: D144N, P164C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
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*TP*GP*TP*GP*CP*T)-3')


Mass: 3010.978 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, 184 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.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH8.5, 200 mM Ca(OAc)2, 18% (wt/vol) 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: 1.81→81.31 Å / Num. obs: 28148 / % possible obs: 99.7 % / Redundancy: 3.6 % / Net I/σ(I): 11.6
Reflection shellResolution: 1.81→1.85 Å / Rmerge(I) obs: 0.112

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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: 1.81→46.354 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2196 1414 5.03 %
Rwork0.1665 --
obs0.1692 28119 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→46.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 404 9 182 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092347
X-RAY DIFFRACTIONf_angle_d1.4743281
X-RAY DIFFRACTIONf_dihedral_angle_d19.106910
X-RAY DIFFRACTIONf_chiral_restr0.046354
X-RAY DIFFRACTIONf_plane_restr0.006359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.87470.29421330.27132628X-RAY DIFFRACTION99.4
1.8747-1.94980.28341510.22772651X-RAY DIFFRACTION100
1.9498-2.03850.26071270.20062681X-RAY DIFFRACTION100
2.0385-2.1460.25011490.19262676X-RAY DIFFRACTION100
2.146-2.28040.23781400.16662616X-RAY DIFFRACTION100
2.2804-2.45650.22181320.16662686X-RAY DIFFRACTION100
2.4565-2.70370.24221250.16362704X-RAY DIFFRACTION100
2.7037-3.09480.19061690.1572630X-RAY DIFFRACTION100
3.0948-3.89880.19551620.13712663X-RAY DIFFRACTION99
3.8988-46.3540.19981260.15222770X-RAY DIFFRACTION99
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)
17.66924.6175-3.48745.0234-5.35567.06870.1796-0.15890.57960.4267-0.07550.9853-0.6214-0.5694-0.10090.24830.0457-0.02890.2071-0.09130.3208-16.10636.3238-10.2208
22.1924-1.5252-1.57587.27241.55465.23-0.0286-0.00090.0174-0.2325-0.08670.0709-0.43340.03270.12020.26140.0003-0.0910.11730.00530.1723-4.94724.1935-29.5589
37.6475-0.26485.96645.6004-0.10838.64-0.4060.36560.7054-0.6456-0.0741-0.4683-0.71330.32150.49950.3224-0.03980.00150.1470.03280.24851.79587.7462-34.8197
48.7595-3.26251.54994.3356-1.67327.71860.08190.96810.2943-0.7435-0.0701-0.1942-0.11870.34670.00150.3634-0.08470.00570.20130.030.18561.9817-0.8039-42.4309
56.06040.97491.17542.35211.41165.1442-0.10130.3082-0.2883-0.31310.00520.18370.2451-0.16890.13840.3252-0.0187-0.08360.1018-0.02010.2274-6.8365-9.965-37.2858
61.1851-0.34830.60940.69830.63242.20650.0558-0.0517-0.09520.0501-0.09030.25440.1432-0.14320.01860.1962-0.0465-0.03290.0987-0.00480.2148-9.5411-5.6623-16.0799
74.6613-1.6126-3.12462.34874.09317.6129-0.0073-0.09490.5810.13360.0855-0.3792-0.17890.3433-0.08240.2271-0.0349-0.05820.10520.01910.2121-1.1986.7835-6.6117
88.4221-5.513-0.31457.63420.53794.1292-0.2265-0.2587-0.04580.7090.0541-0.12180.15710.15620.17920.2642-0.0388-0.02220.07980.03460.1643-2.0446-2.6035-2.2864
91.9783-1.3258-0.13631.2601-0.71213.5165-0.0156-0.33030.0005-0.224-0.277-0.72710.15070.8928-0.01380.2142-0.0134-0.04560.2902-0.03760.301110.4442-11.2568-22.4459
104.5979-1.815-2.74822.1245-0.09242.63050.2373-0.8743-0.1279-0.1379-0.2404-1.10290.09580.2779-0.05010.2675-0.0145-0.09360.20560.05850.45758.9264-11.257-21.0946
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 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 64 )
4X-RAY DIFFRACTION4chain 'A' and (resid 65 through 88 )
5X-RAY DIFFRACTION5chain 'A' and (resid 89 through 124 )
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 196 )
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 210 )
8X-RAY DIFFRACTION8chain 'A' and (resid 211 through 229 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 12 )
10X-RAY DIFFRACTION10chain 'D' and (resid 13 through 22 )

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