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- PDB-6q0c: MutY adenine glycosylase bound to DNA containing a transition sta... -

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Basic information

Entry
Database: PDB / ID: 6q0c
TitleMutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with undamaged dG
Components
  • A/G-specific adenine glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
Keywordshydrolase/DNA / Protein-DNA complex / DNA repair / transition state analog / hydrolase-DNA complex
Function / homology
Function and homology information


adenine glycosylase / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / 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 / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / 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 / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / 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 / DNA glycosylase / Endonuclease III; domain 1 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsO'Shea Murray, V.L. / Russelburg, L.P. / Horvath, M.P. / David, S.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1608934 United States
National Science Foundation (NSF, United States)1610721 United States
Citation
Journal: Acs Chem.Biol. / Year: 2020
Title: Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY.
Authors: Russelburg, L.P. / O'Shea Murray, V.L. / Demir, M. / Knutsen, K.R. / Sehgal, S.L. / Cao, S. / David, S.S. / Horvath, M.P.
#1: Journal: Nucleic Acids Res. / Year: 2016
Title: Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.
Authors: Woods, R.D. / O'Shea, V.L. / Chu, A. / Cao, S. / Richards, J.L. / Horvath, M.P. / David, S.S.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionAug 28, 2019ID: 3FSP
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_database_related.db_id / _pdbx_database_related.details
Revision 1.4Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.5Oct 11, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: A/G-specific adenine glycosylase
B: DNA (5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3')
C: DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8636
Polymers48,4093
Non-polymers4543
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-52 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.860, 86.140, 141.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein A/G-specific adenine glycosylase


Mass: 41810.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: MutY / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P83847, adenine glycosylase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3')


Mass: 3407.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*CP*AP*(NR1)P*GP*TP*CP*T)-3')


Mass: 3191.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 73 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Description: Dark golden-brown rod 50micrometer x 300micrometer
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 500 mM calcium acetate 100 mM Tris pH 8.5 14% PEG 4000 5 mM beta-mercaptoethanol 5% ethylene glycol
Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2008
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2→41.296 Å / Num. obs: 31172 / % possible obs: 97.1 % / Redundancy: 4.442 % / Biso Wilson estimate: 50.065 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.058 / Χ2: 0.987 / Net I/σ(I): 15.52 / Num. measured all: 138458 / Scaling rejects: 638
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.1281.820.525640229118030.3292.17578.7
2.05-2.113.4290.7861.86951229920270.5950.92988.2
2.11-2.173.9130.6421.978237218421050.6250.74396.4
2.17-2.244.7280.4563.0410331218521850.8430.514100
2.24-2.314.8290.3923.719948206020600.8570.44100
2.31-2.394.7710.2864.879794205520530.9310.32299.9
2.39-2.484.8180.2336.059361194519430.9510.26299.9
2.48-2.584.8020.1837.688990187218720.9690.206100
2.58-2.74.7770.1479.458804184518430.9780.16599.9
2.7-2.834.60.15212.467719170816780.9730.17298.2
2.83-2.984.7370.07816.757911167416700.9950.08899.8
2.98-3.164.7420.05522.497488158115790.9970.06199.9
3.16-3.384.6760.04828.796874147614700.9980.05599.6
3.38-3.654.6770.03535.76435137913760.9980.0499.8
3.65-44.6010.0338.915899128312820.9990.03499.9
4-4.474.5410.02742.545340118011760.9990.03199.7
4.47-5.164.3950.02843.374584104710430.9990.03199.6
5.16-6.324.190.0342.237589008970.9980.03499.7
6.32-8.944.1460.02944.0329197127040.9990.03298.9
8.94-41.2963.6330.02542.5614754294060.9990.02994.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.15rc2_3428refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DPK

5dpk
PDB Unreleased entry


Resolution: 2→41.296 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.43
RfactorNum. reflection% reflection
Rfree0.2706 1494 4.83 %
Rwork0.2474 --
obs0.2485 30904 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.65 Å2 / Biso mean: 62.5802 Å2 / Biso min: 21.49 Å2
Refinement stepCycle: final / Resolution: 2→41.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 420 19 71 3223
Biso mean--46.09 46.01 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d03309
X-RAY DIFFRACTIONf_angle_d0.694607
X-RAY DIFFRACTIONf_dihedral_angle_d16.31897
X-RAY DIFFRACTIONf_chiral_restr0.04515
X-RAY DIFFRACTIONf_plane_restr0519
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.06460.5053990.5023192172
2.0646-2.13840.4891210.4308245990
2.1384-2.2240.34411340.32262740100
2.224-2.32520.33231560.29932714100
2.3252-2.44780.29371420.29792733100
2.4478-2.60110.32461430.28382746100
2.6011-2.80190.30781410.2979272999
2.8019-3.08380.28661490.26792771100
3.0838-3.52980.26431310.2332799100
3.5298-4.44640.22531330.20522840100
4.4464-41.2960.22991450.2114295899

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