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

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Basic information

Entry
Database: PDB / ID: 2jhn
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


catalytic activity / base-excision repair
Similarity search - Function
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 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase ...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 / HhH-GPD superfamily base excision DNA repair protein / Hypothetical protein; domain 2 / 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
: / MERCURIBENZOIC ACID / 3-methyladenine DNA glycosylase (AlkA)
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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

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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)70,84918
Polymers68,5632
Non-polymers2,28616
Water8,917495
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A: 3-METHYLADENINE DNA-GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2298
Polymers34,2821
Non-polymers9487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 3-METHYLADENINE DNA-GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,62010
Polymers34,2821
Non-polymers1,3389
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.494, 49.968, 105.798
Angle α, β, γ (deg.)90.00, 107.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 34281.520 Da / Num. of mol.: 2 / Mutation: YES
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

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Non-polymers , 6 types, 511 molecules

#2: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5HgO2
#3: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 229 TO ILE ENGINEERED RESIDUE IN CHAIN B, MET 229 TO ILE
Sequence detailsSINGLE MUTATION M229I

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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 STRUCTURE WAS DETERMINED BY SHARP USING MERCURY SITES IDENTIFIED BY SHELXD. THE ANOMALOUS DIFFERENCES ARE INCLUDED IN THE DEPOSITED STRUCTURE FACTORS.
Crystal growpH: 6 / Details: 50 MM MES, PH6.0., pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.009
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 63551 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→12 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.481 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED BY A PSEUDO-TRANSLATIONAL VECTOR 0.5,0.45,0.5, BUT HAVE BEEN REFINED INDIVDUALLY. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED BY A PSEUDO-TRANSLATIONAL VECTOR 0.5,0.45,0.5, BUT HAVE BEEN REFINED INDIVDUALLY. RESIDUES A291-A292 AND B290- B293 WERE 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
Rfree0.223 3203 5.1 %RANDOM
Rwork0.185 ---
obs0.187 60152 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.2 Å2
2--0.49 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 98 495 5381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225101
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9796865
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3625606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16222.784255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67315926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7351554
X-RAY DIFFRACTIONr_chiral_restr0.0940.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023866
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.22472
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23521
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0381.53086
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51124751
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.33732362
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4784.52114
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.366 227
Rwork0.272 4287

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