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- PDB-1pu6: Crystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII) -

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Basic information

Entry
Database: PDB / ID: 1pu6
TitleCrystal structure of H.pylori 3-methyladenine DNA glycosylase (MagIII)
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 / metal ion binding
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 / DNA glycosylase / Endonuclease III; domain 1 ...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 / DNA glycosylase / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Endonuclease III
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.64 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: Version format compliance
Remark 999SEQUENCE THE DIFFERENCES BETWEEN THE SEQUENCES IN THE PDB ENTRY 1PU6 AND IN THE DATABASE REFERENCE ...SEQUENCE THE DIFFERENCES BETWEEN THE SEQUENCES IN THE PDB ENTRY 1PU6 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

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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)50,7866
Polymers50,4362
Non-polymers3504
Water4,216234
1
A: 3-METHYLADENINE DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3323
Polymers25,2181
Non-polymers1142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-METHYLADENINE DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4543
Polymers25,2181
Non-polymers2362
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2

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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

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.945
SYNCHROTRONNSLS X12C21.0000, 0.9686, 1.0083
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJan 11, 2002
CUSTOM-MADE2CCDJul 19, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2MADMx-ray1
1Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9451
211
30.96861
41.00831
ReflectionResolution: 1.64→50 Å / Num. all: 60643 / Num. obs: 60643 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.099 / Net I/σ(I): 21.8
Reflection shellResolution: 1.64→1.71 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.337 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 6066 / Rmerge(I) obs: 0.337

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.64→24.41 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.326 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.079
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: ANISOU PARAMETERS WERE DERIVED FROM REFINED TLS PARAMETERS (5 TLS GROUPS) AND HELD FIXED DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.18517 3124 5.2 %RANDOM
Rwork0.15126 ---
obs0.15301 57518 99.94 %-
all-57518 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.947 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.32 Å2
2--0.26 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.64→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 1 254 3729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9684799
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.160.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022622
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21515
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.9431.52155
X-RAY DIFFRACTIONr_mcangle_it3.06523439
X-RAY DIFFRACTIONr_scbond_it4.79931402
X-RAY DIFFRACTIONr_scangle_it6.8474.51360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.638→1.681 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.194 150
Rwork0.143 2809
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.185 / Rfactor Rwork: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.602

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