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- PDB-4b22: Unprecedented sculpting of DNA at abasic sites by DNA glycosylase... -

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Basic information

Entry
Database: PDB / ID: 4b22
TitleUnprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2
Components
  • 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'
  • 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
  • MAG2, DNA-3-METHYLADENINE GLYCOSYLASE 2
KeywordsHYDROLASE / HELIX-HAIRPIN-HELIX DNA GLYCOSYLASE HOMOLOGUE
Function / homology
Function and homology information


alkylated DNA binding / DNA-(abasic site) binding / base-excision repair, AP site formation / catalytic activity / 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 / DNA glycosylase / 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 / DNA glycosylase / Endonuclease III; domain 1 / 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 / SYNCHROTRON / OTHER / Resolution: 1.9 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: MAG2, DNA-3-METHYLADENINE GLYCOSYLASE 2
X: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
Y: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)32,9613
Polymers32,9613
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-19 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.480, 84.520, 125.750
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-2081-

HOH

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Components

#1: Protein MAG2, DNA-3-METHYLADENINE GLYCOSYLASE 2 / 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*(3DR)P*CP*AP*TP*CP*GP)-3' / ABASIC DNA


Mass: 3185.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'


Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTALLIZED PROTEIN CONTAIN N-TERMINAL UNCLEAVED HEKSAHISTIDINE 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 27720 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.32 / % possible all: 96

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 1345 4.6 %RANDOM
Rwork0.2805 ---
obs0.2805 26375 95.1 %-
Solvent computationBsol: 41.6549 Å2 / ksol: 0.380027 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.293 Å20 Å20 Å2
2--2.499 Å20 Å2
3---1.794 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 437 0 245 2319
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00579
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_deg1.13309
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.93926
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.97871
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: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3115 123 5.3 %
Rwork0.2408 2178 -
obs--80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP-CUSTOM.PARAMDNA-RNA-CUSTOM.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAMCNS_TOPPAR:ION.TOP

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