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- PDB-1pu8: Crystal structure of H.pylori 3-methyladenine DNA glycosylase (Ma... -

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Basic information

Entry
Database: PDB / ID: 1pu8
TitleCrystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) bound to 1,N6-ethenoadenine
Components3-METHYLADENINE DNA GLYCOSYLASE
KeywordsHYDROLASE / Helix-hairpin-helix / 3-Methyladenine / BASE EXCISION REPAIR / GLYCOSYLASE
Function / homology
Function and homology information


base-excision repair / 4 iron, 4 sulfur cluster binding / endonuclease activity
Similarity search - Function
Helix-hairpin-helix motif / 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 ...Helix-hairpin-helix motif / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / 3H-IMIDAZO[2,1-I]PURINE / Endonuclease III
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsEichman, B.F. / O'Rourke, E.J. / Radicella, J.P. / Ellenberger, T.
Citation
Journal: Embo J. / Year: 2003
Title: Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases
Authors: Eichman, B.F. / O'Rourke, E.J. / Radicella, J.P. / Ellenberger, T.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: A NOVEL 3-METHYLADENINE DNA GLYCOSYLASE FROM HELICOBACTER PYLORI DEFINES A NEW CLASS WITHIN THE ENDONUCLEASE III FAMILY OF BASE EXCISION REPAIR GLYCOSYLASES
Authors: O'ROURKE, E.J. / CHEVALIER, C. / BOITEUX, S. / LABIGNE, A. / IELPI, L. / RADICELLA, J.P.
History
DepositionJun 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999SEQUENCE THE DIFFERENCES BETWEEN THE SEQUENCES IN THE 1PU6 PDB AND IN THE DATABASE REFERENCE ARE ...SEQUENCE THE DIFFERENCES BETWEEN THE SEQUENCES IN THE 1PU6 PDB AND IN THE DATABASE REFERENCE ARE DUE TO THE PARTICULAR H.PYLORI STRAIN. DATABASE REFERENCE REFERS TO H.PYLORI STRAIN J99; MAGIII WAS CLONED FROM H.PYLORI STRAIN 13/5 (SEE REFERENCE 1)

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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)50,9116
Polymers50,4362
Non-polymers4754
Water2,900161
1
A: 3-METHYLADENINE DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4553
Polymers25,2181
Non-polymers2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-METHYLADENINE DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4553
Polymers25,2181
Non-polymers2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.605, 44.399, 81.516
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3-METHYLADENINE DNA GLYCOSYLASE


Mass: 25218.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 13-5 / Production host: Escherichia coli (E. coli) / References: UniProt: O25323
#2: Chemical ChemComp-EA1 / 3H-IMIDAZO[2,1-I]PURINE / 1,N6-ETHENOADENINE


Mass: 159.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5N5
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, HEPES, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
22 %MPD1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.542 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. all: 28226 / Num. obs: 28226 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.084 / Net I/σ(I): 11.5
Reflection shellResolution: 2.13→2.23 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2783 / Rsym value: 0.369 / % possible all: 99.6
Reflection
*PLUS
Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 99.6 % / Num. unique obs: 2783 / Rmerge(I) obs: 0.369

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PU6

1pu6


Resolution: 2.13→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.092 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.185
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.22992 1434 5.1 %RANDOM
Rwork0.20228 ---
all0.20369 26792 --
obs0.20369 26792 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.758 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.44 Å2
2--0.37 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.13→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 32 161 3660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223571
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9744814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2115428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022652
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21826
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6271.52140
X-RAY DIFFRACTIONr_mcangle_it1.16223415
X-RAY DIFFRACTIONr_scbond_it2.03231431
X-RAY DIFFRACTIONr_scangle_it3.0524.51399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.125→2.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 77
Rwork0.264 1524
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6111-0.1287-0.07021.71780.2674.0394-0.099-0.1559-0.12480.0830.0621-0.08350.1550.33850.0370.09490.0408-0.01690.1116-0.00660.1099118.517918.988956.5131
21.51630.15220.47161.95060.69782.05520.00340.0943-0.0851-0.0550.0556-0.08780.03580.1153-0.05890.104-0.00970.01260.11880.00340.1034109.736512.649435.0295
32.4036-0.47110.15362.42020.13473.0448-0.0596-0.2075-0.04560.22410.1013-0.14830.07340.42-0.04170.06910.0282-0.03020.1706-0.01250.0955131.784541.230314.5073
40.99750.05980.05991.56330.55821.68180.00960.0211-0.0234-0.07210.0461-0.09140.01640.0494-0.05570.1008-0.00480.00550.12420.00310.1363120.486235.8708-5.8712
50.06890.0126-0.07810.0608-0.18620.4372-0.0160.0339-0.02340.00650.0084-0.02090.05790.01470.00760.0399-0.012-0.0050.0142-0.02320.0583115.710526.579618.9764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 24
2X-RAY DIFFRACTION1A145 - 216
3X-RAY DIFFRACTION2A25 - 144
4X-RAY DIFFRACTION2A983
5X-RAY DIFFRACTION2A219
6X-RAY DIFFRACTION3B2 - 24
7X-RAY DIFFRACTION3B145 - 216
8X-RAY DIFFRACTION4B25 - 144
9X-RAY DIFFRACTION4B983
10X-RAY DIFFRACTION4B220
11X-RAY DIFFRACTION5A301 - 459
12X-RAY DIFFRACTION5B303 - 461
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.508

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