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- PDB-4ejy: Structure of MBOgg1 in complex with high affinity DNA ligand -

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Basic information

Entry
Database: PDB / ID: 4ejy
TitleStructure of MBOgg1 in complex with high affinity DNA ligand
Components
  • 3-Methyladenine DNA glycosylase
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
  • DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
KeywordsHYDROLASE/DNA / 8-oxoguanine DNA glycosylase / HYDROLASE-DNA complex
Function / homology
Function and homology information


oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / damaged DNA binding
Similarity search - Function
TATA-Binding Protein - #260 / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / 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 ...TATA-Binding Protein - #260 / 8-oxoguanine DNA glycosylase, N-terminal / 8-oxoguanine DNA glycosylase, N-terminal domain / 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 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-(apurinic or apyrimidinic site) lyase
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJiang, T. / Yu, H.J. / Bi, L.J. / Zhang, X.E. / Yang, M.Z.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structures of MBOgg1 in complex with two abasic DNA ligands
Authors: Yu, H.J. / Yang, M.Z. / Zhang, X.E. / Bi, L.J. / Jiang, T.
History
DepositionApr 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-Methyladenine DNA glycosylase
B: 3-Methyladenine DNA glycosylase
C: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
D: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
E: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
F: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7238
Polymers91,6776
Non-polymers462
Water9,044502
1
A: 3-Methyladenine DNA glycosylase
C: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
D: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8624
Polymers45,8393
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-28 kcal/mol
Surface area17290 Å2
MethodPISA
2
B: 3-Methyladenine DNA glycosylase
E: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')
F: DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8624
Polymers45,8393
Non-polymers231
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-20 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.613, 102.884, 67.284
Angle α, β, γ (deg.)90.00, 90.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-Methyladenine DNA glycosylase / 8-oxoguanine-DNA-glycosylase


Mass: 36189.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: AlkA / Production host: Escherichia coli (E. coli)
References: UniProt: Q8R5T9, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*CP*C)-3')


Mass: 4710.045 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*T*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3')


Mass: 4939.203 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 3350, 0.2-0.25M Sodium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0089 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 30, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 52075 / Num. obs: 52075 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.321 / Num. unique all: 5168 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I0W

3i0w


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.46 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE STRUCTURE WAS REFINED ALSO WITH PHENIX.REFINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.25791 2657 5.1 %RANDOM
Rwork0.22237 ---
all0.22417 49342 --
obs0.22417 49342 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.67 Å2 / Biso mean: 37.125 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å21.1 Å2
2--1.6 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 1241 2 502 6451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226251
X-RAY DIFFRACTIONr_angle_refined_deg0.9862.2188719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5585580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20824.167240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16115848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8991528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024312
X-RAY DIFFRACTIONr_mcbond_it0.4361.52866
X-RAY DIFFRACTIONr_mcangle_it0.81224646
X-RAY DIFFRACTIONr_scbond_it0.85733385
X-RAY DIFFRACTIONr_scangle_it1.454.54071
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 197 -
Rwork0.261 3621 -
all-3818 -
obs--98.91 %

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