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- PDB-2jhj: 3-methyladenine dna-glycosylase from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2jhj
Title3-methyladenine dna-glycosylase from Archaeoglobus fulgidus
Components3-METHYLADENINE DNA-GLYCOSYLASE
KeywordsHYDROLASE / ALKA / DNA REPAIR / N1-METHYLADENINE / N3-METHYLCYTOSINE / HYPERTHERMOPHILES / ARCHAEOGLOBUS FULGIDUS
Function / homology
Function and homology information


DNA-7-methylguanine glycosylase activity / alkylated DNA binding / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex
Similarity search - Function
: / AfAlkA-like, TATA-box binding protein-like domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily / : / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / 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 ...: / AfAlkA-like, TATA-box binding protein-like domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily / : / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / 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 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-methyladenine DNA glycosylase (AlkA)
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. ...Leiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. / Andersen, O.A. / Birkeland, N.K. / Ruoff, P. / Klungland, A. / Bjelland, S.
CitationJournal: Embo J. / Year: 2007
Title: Structural Basis for Enzymatic Excision of N1-Methyladenine and N3-Methylcytosine from DNA
Authors: Leiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. / Andersen, O.A. / Birkeland, N.K. / Ruoff, P. / ...Authors: Leiros, I. / Nabong, M.P. / Grosvik, K. / Ringvoll, J. / Haugland, G.T. / Uldal, L. / Reite, K. / Olsbu, I.K. / Knaevelsrud, I. / Moe, E. / Andersen, O.A. / Birkeland, N.K. / Ruoff, P. / Klungland, A. / Bjelland, S.
History
DepositionFeb 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-METHYLADENINE DNA-GLYCOSYLASE
B: 3-METHYLADENINE DNA-GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,05910
Polymers68,5992
Non-polymers4608
Water10,287571
1
A: 3-METHYLADENINE DNA-GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5305
Polymers34,3001
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 3-METHYLADENINE DNA-GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5305
Polymers34,3001
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.890, 48.850, 104.460
Angle α, β, γ (deg.)90.00, 106.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-METHYLADENINE DNA-GLYCOSYLASE / ALKA


Mass: 34299.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: VC 16 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O28163, DNA-3-methyladenine glycosylase II
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / 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: 2.7 Å3/Da / Density % sol: 54 %
Description: THE STARTING MODEL WAS A MERCURY DERIVATIVE SOLVED BY SAD
Crystal growDetails: 0.1M BICINE, PH9.0 10% W/V PEG20000 2% V/V DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.919
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 53742 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

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

2jhn


Resolution: 1.9→12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.333 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A290-A294 AND B290-B293 ARE DISORDERED THE TWO PROTEIN MONOMERS IN THE ASYMMETRIC UNIT ARE RELATED BY A PSEUDO-TRANSLATIONAL VECTOR (0.5, 0. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A290-A294 AND B290-B293 ARE DISORDERED THE TWO PROTEIN MONOMERS IN THE ASYMMETRIC UNIT ARE RELATED BY A PSEUDO-TRANSLATIONAL VECTOR (0.5, 0.45, 0.5). THE TWO MONOMERS WERE REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2711 5.1 %RANDOM
Rwork0.181 ---
obs0.184 50786 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.19 Å2
2--0.18 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 28 571 5361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224953
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9616658
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74522.648253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67315905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7341555
X-RAY DIFFRACTIONr_chiral_restr0.0910.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023775
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22495
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23429
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2465
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.281
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0551.53031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53324660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.43932253
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7344.51998
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 196
Rwork0.247 3666

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