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- PDB-1kg3: Crystal structure of the core fragment of MutY from E.coli at 1.5... -

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Basic information

Entry
Database: PDB / ID: 1kg3
TitleCrystal structure of the core fragment of MutY from E.coli at 1.55A resolution
ComponentsA/G-specific adenine glycosylase
KeywordsHYDROLASE / DNA Repair
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
IRON/SULFUR CLUSTER / Adenine DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference fourier / Resolution: 1.55 Å
AuthorsGilboa, R. / Kilshtein, A. / Zharkov, D.O. / Kycia, J.H. / Gerchman, S.E. / Grollman, A.P. / Shoham, G.
Citation
Journal: To be Published
Title: Analysis of the E.coli MutY DNA glycosylase structure and function by site-directed mutagenesis
Authors: Gilboa, R. / Kilshtein, A. / Zharkov, D.O. / Kycia, J.H. / Gerchman, S.E. / Grollman, A.P. / Shoham, G.
#1: Journal: Biochemistry / Year: 2000
Title: Role for Lysine 142 in the excision of adenine from A:G mispairs by MutY DNA glycosylase of Escherichia coli.
Authors: Zharkov, D.O. / Gilboa, R. / Yagil, I. / Kycia, J.H. / Gerchman, S.E. / Shoham, G. / Grollmam, A.P.
History
DepositionNov 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 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_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_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_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

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Assembly

Deposited unit
A: A/G-specific adenine glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9658
Polymers25,0491
Non-polymers9167
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.450, 50.200, 70.500
Angle α, β, γ (deg.)90.00, 123.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein A/G-specific adenine glycosylase


Mass: 25048.990 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mutY / Plasmid: pET13a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P17802, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 1.81 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Lithium sulfate, HEPES, Sodium chloride, Magnesium sulfate. Different crystallization concentration in comparison to 1kg2., pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→43 Å / Num. all: 35337 / Num. obs: 35337 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.2 Å2 / Rsym value: 0.043 / Net I/σ(I): 17.2
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4 % / Num. unique all: 1936 / Rsym value: 0.25 / % possible all: 97.6

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: difference fourier
Starting model: 1KG2

1kg2


Resolution: 1.55→43 Å / Num. parameters: 8297 / Num. restraintsaints: 7588 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: CNS 0.9 WAS ALSO USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1724 5.2 %RANDOM
Rwork0.1722 ---
all-35337 --
obs-35337 98.7 %-
Displacement parametersBiso mean: 24.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å / Num. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2001.52
Refinement stepCycle: LAST / Resolution: 1.55→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 41 212 2005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0.069
X-RAY DIFFRACTIONs_from_restr_planes0.0231
X-RAY DIFFRACTIONs_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.065
X-RAY DIFFRACTIONs_approx_iso_adps0

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