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- PDB-2abk: REFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOL... -

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Basic information

Entry
Database: PDB / ID: 2abk
TitleREFINEMENT OF THE NATIVE STRUCTURE OF ENDONUCLEASE III TO A RESOLUTION OF 1.85 ANGSTROM
ComponentsENDONUCLEASE III
KeywordsENDONUCLEASE / DNA-REPAIR / DNA GLYCOSYLASE
Function / homology
Function and homology information


oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation via deaminated base removal / base-excision repair, AP site formation / DNA N-glycosylase activity / uracil DNA N-glycosylase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to UV / 4 iron, 4 sulfur cluster binding ...oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation via deaminated base removal / base-excision repair, AP site formation / DNA N-glycosylase activity / uracil DNA N-glycosylase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to UV / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
Endonuclease III / Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Iron-sulfur binding domain of endonuclease III / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif ...Endonuclease III / Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / Iron-sulfur binding domain of endonuclease III / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Endonuclease III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsThayer, M.M. / Tainer, J.A.
Citation
Journal: EMBO J. / Year: 1995
Title: Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
Authors: Thayer, M.M. / Ahern, H. / Xing, D. / Cunningham, R.P. / Tainer, J.A.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Crystallographic Characterization of the Iron-Sulfur Containing DNA-Repair Enzyme Endonuclease III from Escherichia Coli Enzyme Endonuclease III
Authors: Kuo, C.-F. / Mcree, D.E. / Cunningham, R.P. / Tainer, J.A.
#2: Journal: Science / Year: 1992
Title: Atomic Structure of the DNA Repair [4Fe-4S] Enzyme Endonuclease III
Authors: Kuo, C.-F. / Mcree, D.E. / Fisher, C.L. / Handley, S. / Cunningham, R.P. / Tainer, J.A.
History
DepositionMay 11, 1995Processing site: BNL
SupersessionOct 15, 1995ID: 1ABK
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED BY PROCHECK FOLLOWED BY VISUAL ...HELIX DETERMINATION METHOD: KABSCH AND SANDER AS IMPLEMENTED BY PROCHECK FOLLOWED BY VISUAL INSPECTION OF MODEL. TURN KABSCH AND SANDER IN PROCHECK TURN_ID: FG, HAIRPIN OF HELIX HAIRPIN HELIX MOTIF.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDONUCLEASE III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9472
Polymers23,5951
Non-polymers3521
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.500, 65.800, 86.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENDONUCLEASE III


Mass: 23595.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: UC 6444 DELTA NTH
References: UniProt: P0AB83, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMHEPES11
2150 mM11NaCl
35 %glycerol11

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: May 18, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 27787 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.07
Reflection
*PLUS
Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
XENGENdata reduction
X-PLOR3phasing
RefinementResolution: 1.85→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.216 -10 %
Rwork0.185 --
obs0.185 26043 93.1 %
Displacement parametersBiso mean: 23.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 8 123 1798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16

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