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- PDB-2yg9: Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka)... -

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Basic information

Entry
Database: PDB / ID: 2yg9
TitleStructure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans
ComponentsDNA-3-methyladenine glycosidase II, putative
KeywordsHYDROLASE / DNA REPAIR
Function / homology
Function and homology information


DNA-7-methylguanine glycosylase activity / alkylated DNA binding / DNA-3-methyladenine glycosylase activity / DNA-3-methyladenine glycosylase II / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex / cytoplasm
Similarity search - Function
Endonuclease Iii, domain 2 - #40 / : / 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 ...Endonuclease Iii, domain 2 - #40 / : / 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
NICKEL (II) ION / DNA-3-methyladenine glycosylase II
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMoe, E. / Hall, D.R. / Leiros, I. / Talstad, V. / Timmins, J. / McSweeney, S.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans.
Authors: Moe, E. / Hall, D.R. / Leiros, I. / Monsen, V.T. / Timmins, J. / McSweeney, S.
History
DepositionApr 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references / Non-polymer description / Version format compliance
Revision 1.2Jun 20, 2012Group: Other
Revision 1.3Dec 5, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct / struct_ref
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _struct.title / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-3-methyladenine glycosidase II, putative
B: DNA-3-methyladenine glycosidase II, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0089
Polymers47,6572
Non-polymers3517
Water11,025612
1
A: DNA-3-methyladenine glycosidase II, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0505
Polymers23,8281
Non-polymers2224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-3-methyladenine glycosidase II, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9584
Polymers23,8281
Non-polymers1303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.311, 51.372, 90.039
Angle α, β, γ (deg.)90.00, 99.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2104-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.94456, -0.0149, 0.32801), (-0.01474, -0.99989, -0.00295), (0.32802, -0.00205, -0.94467)
Vector: -21.21795, -15.26268, 124.27422)

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Components

#1: Protein DNA-3-methyladenine glycosidase II, putative


Mass: 23828.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_2584 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: Q9RRB0
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.44 Å3/Da / Density % sol: 49.6 % / Description: NONE
Crystal growDetails: 1 UL DROPS OF 10 MG/ML PROTEIN MIXED WITH A SOLUTION CONTAINING 1 M LICL2, 0.1 M MES PH 6.0 AND 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Details: MIRROR
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→42.68 Å / Num. obs: 35790 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 12.76 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YG8

2yg8


Resolution: 1.95→42.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.454 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23101 1802 5 %RANDOM
Rwork0.17011 ---
obs0.17315 33988 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 12 612 3697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223207
X-RAY DIFFRACTIONr_bond_other_d0.0020.022193
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9794391
X-RAY DIFFRACTIONr_angle_other_deg1.01735316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8175425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50722.109128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19515478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6731534
X-RAY DIFFRACTIONr_chiral_restr0.090.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023643
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_nbd_refined0.2130.2720
X-RAY DIFFRACTIONr_nbd_other0.2040.22272
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21568
X-RAY DIFFRACTIONr_nbtor_other0.0870.21683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0131.52619
X-RAY DIFFRACTIONr_mcbond_other0.2121.5842
X-RAY DIFFRACTIONr_mcangle_it1.2823314
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.34331296
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5284.51070
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 125 -
Rwork0.2 2533 -
obs--99.92 %

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