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- PDB-1kea: STRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE -

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Basic information

Entry
Database: PDB / ID: 1kea
TitleSTRUCTURE OF A THERMOSTABLE THYMINE-DNA GLYCOSYLASE
ComponentsPossible G-T mismatches repair enzyme
KeywordsHYDROLASE / DNA Repair / DNA Glycosylase / DNA Mismatch / Methylation / Base Twisting
Function / homology
Function and homology information


thymine-DNA glycosylase / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / 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. / Endonuclease III-like, iron-sulphur cluster loop motif / FES / 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 ...Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Endonuclease III-like, iron-sulphur cluster loop motif / FES / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / IRON/SULFUR CLUSTER / Thymine/uracil-DNA glycosylase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMol, C.D. / Arvai, A.S. / Begley, T.J. / Cunningham, R.P. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases.
Authors: Mol, C.D. / Arvai, A.S. / Begley, T.J. / Cunningham, R.P. / Tainer, J.A.
History
DepositionNov 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_symmetry / _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: Possible G-T mismatches repair enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1689
Polymers25,4441
Non-polymers7248
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Possible G-T mismatches repair enzyme
hetero molecules

A: Possible G-T mismatches repair enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,33618
Polymers50,8882
Non-polymers1,44816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4750 Å2
ΔGint-153 kcal/mol
Surface area21180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.215, 68.215, 98.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-5016-

HOH

DetailsThe biologically active structure is a monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Possible G-T mismatches repair enzyme / Mismatch Glycosylase


Mass: 25443.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli)
References: UniProt: P29588, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 5 types, 208 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8
Details: ammonium sulfate, zinc acetate, hepes, pH 8.0, EVAPORATION, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
210 mMHEPES-NaOH1droppH7.5
3100 mM1dropNaCl
460 %satammonium sulfate1reservoir
5100 mMHEPES1reservoirpH8.0
610 mMzinc acetate1reservoir
72 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 28, 1998
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 16125 / Num. obs: 16125 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.4 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 209829 / Rmerge(I) obs: 0.066

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.77 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1194575.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 778 4.8 %RANDOM
Rwork0.211 ---
all0.2124 16125 --
obs0.211 16107 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7013 Å2 / ksol: 0.351786 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å20 Å20 Å2
2--2.1 Å20 Å2
3----4.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 27 200 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.61.5
X-RAY DIFFRACTIONc_mcangle_it1.052
X-RAY DIFFRACTIONc_scbond_it0.882
X-RAY DIFFRACTIONc_scangle_it1.412.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 127 5.1 %
Rwork0.237 2365 -
obs--93.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PAR.FS4
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
X-RAY DIFFRACTIONc_mcbond_it0.61.5
X-RAY DIFFRACTIONc_scbond_it0.882
X-RAY DIFFRACTIONc_mcangle_it1.052
X-RAY DIFFRACTIONc_scangle_it1.412.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.251 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.237

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