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- PDB-4b21: Unprecedented sculpting of DNA at abasic sites by DNA glycosylase... -

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Basic information

Entry
Database: PDB / ID: 4b21
TitleUnprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2
Components
  • 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'
  • 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*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 / catalytic activity / protein-DNA complex / DNA binding / nucleus / cytoplasm
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
beta-D-glucopyranose / PHOSPHATE ION / DNA / DNA (> 10) / Alkylbase DNA glycosidase-like protein mag2
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 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 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*GP*AP*TP*CP*GP)-3'
Y: 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1377
Polymers32,6723
Non-polymers4654
Water4,594255
1
A: PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2
X: 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3'
Y: 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)66,27514
Polymers65,3446
Non-polymers9308
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11910 Å2
ΔGint-80.4 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.926, 84.746, 126.713
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-2075-

HOH

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Components

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DNA chain , 2 types, 2 molecules XY

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


Mass: 3225.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP)-3'


Mass: 3085.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Protein / Sugars , 2 types, 2 molecules A

#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
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 258 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

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 / Number of used crystals: 1

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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: ALS / Beamline: 8.3.1 / Wavelength: 1.11
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 62545 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 28.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 15.2
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 3171 4.8 %RANDOM
Rwork0.2069 ---
obs0.2069 59374 94.8 %-
Solvent computationBsol: 70.8735 Å2 / ksol: 0.42927 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.028 Å20 Å20 Å2
2--0.11 Å20 Å2
3---2.918 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 418 27 255 2352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004726
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_deg1.33364
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 1.45→1.5 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 279 5.4 %
Rwork0.2862 5129 -
obs--82.9 %
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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