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- PDB-1mpg: 3-METHYLADENINE DNA GLYCOSYLASE II FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1mpg
Title3-METHYLADENINE DNA GLYCOSYLASE II FROM ESCHERICHIA COLI
Components3-METHYLADENINE DNA GLYCOSYLASE II
KeywordsHYDROLASE / DNA GLYCOSYLASE / DNA REPAIR / BASE EXCISION / METHYLATION / ALKA
Function / homology
Function and homology information


alkylated DNA binding / alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex ...alkylated DNA binding / alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex / base-excision repair / DNA repair / DNA damage response / cytoplasm
Similarity search - Function
DNA-3-methyladenine glycosylase AlkA, N-terminal / AlkA N-terminal domain / AlkA N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 ...DNA-3-methyladenine glycosylase AlkA, N-terminal / AlkA N-terminal domain / AlkA N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain / DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily / Alkylbase DNA glycosidase, conserved site / Alkylbase DNA glycosidases alkA family signature. / 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 / DNA glycosylase / Endonuclease III; domain 1 / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-3-methyladenine glycosylase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD, SIRAS / Resolution: 1.8 Å
AuthorsLabahn, J. / Schaerer, O.D. / Long, A. / Ezaz-Nikpay, K. / Verdine, G.L. / Ellenberger, T.E.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Structural basis for the excision repair of alkylation-damaged DNA.
Authors: Labahn, J. / Scharer, O.D. / Long, A. / Ezaz-Nikpay, K. / Verdine, G.L. / Ellenberger, T.E.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Three-Dimensional Structure of a DNA Repair Enzyme, 3-Methyladenine DNA Glycosylase II, from Escherichia Coli
Authors: Yamagata, Y. / Kato, M. / Odawara, K. / Tokuno, Y. / Nakashima, Y. / Matsushima, N. / Yasumura, K. / Tomita, K.I. / Ihara, K. / Fujii, Y. / Nakabeppu, Y. / Sekiguchi, M. / Fujii, S.
History
DepositionOct 28, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-METHYLADENINE DNA GLYCOSYLASE II
B: 3-METHYLADENINE DNA GLYCOSYLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0354
Polymers62,8502
Non-polymers1842
Water6,017334
1
A: 3-METHYLADENINE DNA GLYCOSYLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5172
Polymers31,4251
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-METHYLADENINE DNA GLYCOSYLASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5172
Polymers31,4251
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.080, 75.770, 60.920
Angle α, β, γ (deg.)90.00, 109.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99861, -0.05267, 0.00164), (0.0527, 0.99797, -0.03583), (0.00025, 0.03586, 0.99936)
Vector: -26.43093, -40.12708, -1.96037)

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Components

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


Mass: 31425.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Gene: ALKA / Plasmid: PKEN2ALKA / Cellular location (production host): CYTOPLASM / Gene (production host): ALKA / Production host: Escherichia coli (E. coli) / Strain (production host): XA90
References: UniProt: P04395, DNA-3-methyladenine glycosylase II
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.01 Å3/Da / Density % sol: 38.61 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 4% PEG 8000, 50 MM NACL, 10 MM TRIS-CL (PH 7.5), 7.5 MM KPO4 (PH 5.9),0.1 MM EDTA, 1.5 MM DITHIOTHREITOL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlprotein1drop
20.05 M1dropNaCl
30.01 MTris-Cl1drop
41.5 mMdithiothreitol1drop
50.05 mMEDTA1drop
60.0075 Mpotassium phosphate1drop
73-5 %(w/v)PEG80001drop
80.015 Mpotassium phosphate1reservoir
96-10 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 45971 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 12 / Rsym value: 0.133 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 318470

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD, SIRAS / Resolution: 1.8→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: CHAIN A AND CHAIN B WERE REFINED WITHOUT NCS RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4541 9.94 %RANDOM
Rwork0.194 ---
obs0.194 45059 98.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.89 Å20 Å22.15 Å2
2--3.67 Å20 Å2
3---2.32 Å2
Refine analyzeLuzzati d res low obs: 30 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4406 0 12 334 4752
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.541.5
X-RAY DIFFRACTIONx_mcangle_it2.232
X-RAY DIFFRACTIONx_scbond_it3.022
X-RAY DIFFRACTIONx_scangle_it4.362.5
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.312 523 9.3 %
Rwork0.265 4909 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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