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- PDB-4b24: Unprecedented sculpting of DNA at abasic sites by DNA glycosylase... -

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Basic information

Entry
Database: PDB / ID: 4b24
TitleUnprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2
Components
  • 5'-D(*CP*GP*AP*TP*AP*GP*GP*TP*AP*GP)-3'
  • 5'-D(*GP*CP*TP*AP*CP*3DRP*TP*AP*TP*CP*GP)-3'
  • PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / HELIX-HAIRPIN-HELIX
Function / homology
Function and homology information


alkylated DNA binding / DNA-(abasic site) binding / base-excision repair, AP site formation / protein-DNA complex / DNA binding / nucleus
Similarity search - Function
Endonuclease Iii, domain 2 - #40 / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / : / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 ...Endonuclease Iii, domain 2 - #40 / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / : / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Alkylbase DNA glycosidase-like protein mag2
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.3 Å
AuthorsDalhus, B. / Nilsen, L. / Korvald, H. / Huffman, J. / Forstrom, R.J. / McMurray, C.T. / Alseth, I. / Tainer, J.A. / Bjoras, M.
CitationJournal: Structure / Year: 2013
Title: Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2.
Authors: Dalhus, B. / Nilsen, L. / Korvald, H. / Huffman, J. / Forstrom, R.J. / Mcmurray, C.T. / Alseth, I. / Tainer, J.A. / Bjoras, M.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2
X: 5'-D(*GP*CP*TP*AP*CP*3DRP*TP*AP*TP*CP*GP)-3'
Y: 5'-D(*CP*GP*AP*TP*AP*GP*GP*TP*AP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)32,6713
Polymers32,6713
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-18.7 kcal/mol
Surface area13050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.650, 84.650, 125.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2100-

HOH

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Components

#1: Protein PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2 / MAG2\ / 3-METHYLADENINE DNA GLYCOSIDASE / 2\ / 3MEA DNA GLYCOSYLASE 2


Mass: 26362.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O94468, DNA-3-methyladenine glycosylase II
#2: DNA chain 5'-D(*GP*CP*TP*AP*CP*3DRP*TP*AP*TP*CP*GP)-3'


Mass: 3200.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*CP*GP*AP*TP*AP*GP*GP*TP*AP*GP)-3'


Mass: 3109.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLIZED PROTEIN CONTAINS N-TERMINAL UNCLEAVED HEXAHISTIDINE TAG (MGSSHHHHHSSGLVPRGSH)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 0.40 M (NH4)H2PO4 (NOT PH ADJUSTED), 6% 1,6-HEXANEDIOL

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15958 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.13 / Net I/σ(I): 4.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.36 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.3→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 789 4.7 %RANDOM
Rwork0.237 ---
obs0.237 15169 95.6 %-
Solvent computationBsol: 48.746 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--8.233 Å20 Å20 Å2
2--5.349 Å20 Å2
3---2.884 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 418 0 146 2210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0064
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_deg1.163
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.315
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.0395
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.357 86 5.6 %
Rwork0.286 1436 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-CUSTOM.PARAMDNA-RNA-CUSTOM.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAMCNS_TOPPAR:ION.TOP
X-RAY DIFFRACTION5GLE.PARGLE.TOP

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