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- PDB-1mun: CATALYTIC DOMAIN OF MUTY FROM ESCHERICHIA COLI D138N MUTANT -

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Basic information

Entry
Database: PDB / ID: 1mun
TitleCATALYTIC DOMAIN OF MUTY FROM ESCHERICHIA COLI D138N MUTANT
ComponentsADENINE GLYCOSYLASE
KeywordsDNA REPAIR / DNA G.A MISMATCH REPAIR ENZYME / GLYCOSIDASE / HYDROLASE
Function / homology
Function and homology information


adenine/guanine mispair binding / adenine glycosylase / 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 / metal ion binding
Similarity search - Function
Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / 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, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / 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 / NUDIX hydrolase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / IRON/SULFUR CLUSTER / Adenine DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGuan, Y. / Tainer, J.A.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily.
Authors: Guan, Y. / Manuel, R.C. / Arvai, A.S. / Parikh, S.S. / Mol, C.D. / Miller, J.H. / Lloyd, S. / Tainer, J.A.
History
DepositionAug 26, 1998Processing site: BNL
Revision 1.0Aug 26, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENINE GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8378
Polymers25,0481
Non-polymers7897
Water6,143341
1
A: ADENINE GLYCOSYLASE
hetero molecules

A: ADENINE GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,67416
Polymers50,0962
Non-polymers1,57814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)82.500, 49.000, 69.400
Angle α, β, γ (deg.)90.00, 122.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1167-

HOH

21A-1237-

HOH

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Components

#1: Protein ADENINE GLYCOSYLASE


Mass: 25048.004 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: D138N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
References: UniProt: P17802, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2400 mM1dropNaCl
320 %glycerol1drop
42.2 Mammonium sulfate1drop
5100 mMimidazole/malate1drop

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 65781 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.053
Reflection shellHighest resolution: 1.2 Å
Reflection
*PLUS
Num. measured all: 137211 / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE MUTY

Resolution: 1.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.169 -10 %10%
obs0.124 -91 %-
all-65714 --
Refine analyzeNum. disordered residues: 8
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 39 341 2142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.124
Solvent computation
*PLUS
Displacement parameters
*PLUS

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