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- PDB-1k3w: Crystal structure of a trapped reaction intermediate of the DNA R... -

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Basic information

Entry
Database: PDB / ID: 1k3w
TitleCrystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA
Components
  • 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'
  • Endonuclease VIII
KeywordsHYDROLASE/DNA / HYDROLASE-DNA complex
Function / homology
Function and homology information


oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Endonuclease VIII / Nei, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal ...Endonuclease VIII / Nei, N-terminal / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease 8
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.42 Å
AuthorsGolan, G. / Zharkov, D.O. / Gilboa, R. / Fernandes, A.S. / Kycia, J.H. / Gerchman, S.E. / Rieger, R.A. / Grollman, A.P. / Shoham, G.
CitationJournal: EMBO J. / Year: 2002
Title: Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.
Authors: Zharkov, D.O. / Golan, G. / Gilboa, R. / Fernandes, A.S. / Gerchman, S.E. / Kycia, J.H. / Rieger, R.A. / Grollman, A.P. / Shoham, G.
History
DepositionOct 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'
C: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
A: Endonuclease VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9917
Polymers37,6373
Non-polymers3544
Water7,152397
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.030, 76.030, 164.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-846-

HOH

21A-849-

HOH

31A-975-

HOH

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain 5'-D(*GP*GP*CP*TP*TP*CP*AP*TP*CP*CP*TP*GP*G)-3'


Mass: 3958.571 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'


Mass: 3863.531 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein Endonuclease VIII


Mass: 29814.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nei / Plasmid: pET13a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P50465, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 3 types, 401 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M Ammonium-sulfate, 0.1M sodium-citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion / PH range low: 5 / PH range high: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mMTris-HCl1drop
25 mM1dropMgCl2
4460 mM1dropNaCl
51.8-2.0 mg/mlprotein1drop
61.8 Mammonium sulfate1reservoir
70.1 Msodium acetate1reservoirpH4.6-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.42→40 Å / Num. obs: 86586 / % possible obs: 95.2 % / Redundancy: 5.5 % / Rsym value: 0.083 / Net I/σ(I): 8.9
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 2 % / Num. unique all: 3191 / Rsym value: 0.375 / % possible all: 71.4
Reflection
*PLUS
Num. measured all: 471081 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 71.4 % / Rmerge(I) obs: 0.375

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementStarting model: initial MODEL OF BR-URACIL-CONTAINING DNA COMPLEXED WITH ENDONUCLEASE VIII AT 2.4A RESOLUTION

Resolution: 1.42→10 Å / Num. parameters: 25384 / Num. restraintsaints: 31207 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 8521 11.2 %RANDOM
Rwork0.1646 ---
all-76108 --
obs-76108 95.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 338 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2830.41
Refinement stepCycle: LAST / Resolution: 1.42→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 381 16 397 2874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0255
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.092
LS refinement shellResolution: 1.42→1.44 Å
RfactorNum. reflection% reflection
Rfree0.202 8521 11 %
Rwork0.164 --
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor all: 0.165 / Rfactor Rfree: 0.2026 / Rfactor Rwork: 0.1646
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.249
LS refinement shell
*PLUS
Rfactor Rfree: 0.202 / Rfactor Rwork: 0.164

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