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- PDB-6u7t: MutY adenine glycosylase bound to DNA containing a transition sta... -

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Basic information

Entry
Database: PDB / ID: 6u7t
TitleMutY adenine glycosylase bound to DNA containing a transition state analog (1N) paired with d(8-oxo-G)
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*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 / HYDROLASE
Function / homology
Function and homology information


adenine/guanine mispair binding / adenine glycosylase / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair 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 / 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 / Endonuclease III; domain 1 / DNA glycosylase / 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. / Cao, S. / 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
DepositionSep 3, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionOct 2, 2019ID: 5DPK
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Dec 25, 2019Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
Revision 2.1Jan 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 2.2Oct 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: Adenine DNA glycosylase
B: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*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)48,8576
Polymers48,4253
Non-polymers4323
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-61 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.800, 86.490, 140.580
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 Adenine DNA glycosylase / oxoG:A-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*(8OG)P*TP*GP*GP*AP*C)-3')


Mass: 3423.249 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 , 3 types, 78 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.: 75 / 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: 50.54 %
Description: Dark golden-brown rod 75 micrometer x 350 micrometer
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: MICRO-SEEDED, 0.5 M CALCIUM ACETATE, 0.1 M TRIS, 14% W/V PEG4000, 0.005 M BETA-MERCAPTOETHANOL, 5% W/V 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→41.334 Å / Num. obs: 30197 / % possible obs: 94.1 % / Redundancy: 6.523 % / Biso Wilson estimate: 41.487 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.09 / Χ2: 1.022 / Net I/σ(I): 15.5 / Num. measured all: 196963 / Scaling rejects: 116
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
2-2.052.6411.0080.983996233115130.3681.24364.9
2.05-2.113.1110.7681.455179228916650.4790.91372.7
2.11-2.175.2840.8681.9710558218319980.6330.95591.5
2.17-2.247.3120.7182.8815305216920930.820.77296.5
2.24-2.317.2270.5833.614946206920680.8630.627100
2.31-2.397.3030.4714.3914424203119750.9170.50797.2
2.39-2.487.2290.3935.4314082194819480.9330.423100
2.48-2.587.3270.3046.8413409186918300.9530.32897.9
2.58-2.77.1950.2418.3413238186318400.9660.2698.8
2.7-2.837.3270.18510.8612331168816830.9840.19999.7
2.83-2.987.1430.13514.3311801167016520.9910.14698.9
2.98-3.167.1240.0920.1711135157715630.9960.09899.1
3.16-3.387.1390.06127.2210580148214820.9980.066100
3.38-3.656.9730.04933.729504137013630.9990.05399.5
3.65-46.9180.04338.078828128212760.9990.04699.5
4-4.476.8050.03743.317982117411730.9990.0499.9
4.47-5.166.6480.03545.046927104510420.9990.03899.7
5.16-6.326.4240.03543.4558209069060.9990.038100
6.32-8.946.4690.03147.545547067040.9990.03399.7
8.94-41.3345.5890.02448.9323644284230.9990.02698.8

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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: 1RRQ

1rrq


Resolution: 2→41.334 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.6
RfactorNum. reflection% reflection
Rfree0.2702 1456 4.82 %
Rwork0.2614 --
obs0.2618 30194 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.89 Å2 / Biso mean: 49.0743 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: final / Resolution: 2→41.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 421 10 75 3246
Biso mean--46.4 35.22 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053300
X-RAY DIFFRACTIONf_angle_d0.7354584
X-RAY DIFFRACTIONf_dihedral_angle_d19.2391898
X-RAY DIFFRACTIONf_chiral_restr0.045505
X-RAY DIFFRACTIONf_plane_restr0.004522
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.07150.4199990.3803196866
2.0715-2.15440.40241250.372248883
2.1544-2.25240.39451470.3624291597
2.2524-2.37120.36541700.3397293598
2.3712-2.51970.32221530.3205298899
2.5197-2.71420.28711490.3081300899
2.7142-2.98730.31681630.2977299799
2.9873-3.41940.24271480.25933078100
3.4194-4.30740.22661460.21913097100
4.3074-41.3340.21471560.20943264100

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