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- PDB-1pvs: 3-methyladenine Glcosylase II(AlkA) Hypoxanthine complex -

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Basic information

Entry
Database: PDB / ID: 1pvs
Title3-methyladenine Glcosylase II(AlkA) Hypoxanthine complex
ComponentsDNA-3-methyladenine glycosylase II
KeywordsHYDROLASE / AlkA / hypoxanthine / DNA glycosylase / DNA repair / reaction-product complex
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
7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE / DNA-3-methyladenine glycosylase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTeale, M.
CitationJournal: Bioconjug.Chem. / Year: 2002
Title: 3-methyladenine-DNA glycosylase II: the crystal structure of an AlkA-hypoxanthine complex suggests the possibility of product inhibition.
Authors: Teale, M. / Symersky, J. / DeLucas, L.
History
DepositionJun 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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: DNA-3-methyladenine glycosylase II
B: DNA-3-methyladenine glycosylase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1234
Polymers62,8502
Non-polymers2722
Water4,071226
1
A: DNA-3-methyladenine glycosylase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,4251
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-3-methyladenine glycosylase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5612
Polymers31,4251
Non-polymers1361
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.005, 75.979, 61.417
Angle α, β, γ (deg.)90.00, 110.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-3-methyladenine glycosylase II / / 3-methyladenine-DNA glycosylase II / inducible / TAG II / DNA-3-methyladenine glycosidase II


Mass: 31425.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ALKA OR AIDA OR B2068 / Production host: Escherichia coli (E. coli)
References: UniProt: P04395, DNA-3-methyladenine glycosylase II
#2: Chemical ChemComp-7HP / 7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE


Mass: 136.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.02 Å3/Da / Density % sol: 39.16 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.39→19.77 Å / Num. all: 19046 / Num. obs: 19046 / Observed criterion σ(F): 2 / Biso Wilson estimate: 9.7 Å2 / Limit h max: 22 / Limit h min: -24 / Limit k max: 31 / Limit k min: -24 / Limit l max: 25 / Limit l min: 0 / Observed criterion F max: 469940.18 / Observed criterion F min: 0.45

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→14.99 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1734 9.8 %random
Rwork0.232 ---
all-17875 --
obs-17875 90.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 20.6971 Å2 / ksol: 0.335713 e/Å3
Displacement parametersBiso max: 44.42 Å2 / Biso mean: 14.63 Å2 / Biso min: 1.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.91 Å20 Å20.84 Å2
2--0.22 Å20 Å2
3---1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.2 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 20 226 4676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg21.8
X-RAY DIFFRACTIONx_torsion_impr_deg1.27
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Num. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.512098.50.25319070.0172453211686.2
2.51-2.642419.80.24119800.0152456222190.4
2.64-2.82088.50.23520220.0162435223091.5
2.8-3.022068.40.24620610.0172439226792.9
3.02-3.3221990.25520650.0172438228493.7
3.32-3.7919780.22719130.0162466211085.6
3.79-4.752429.80.2120540.0142467229693.1
4.75-14.992128.50.2120050.0142502221788.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3hypo.paramhypo.top
X-RAY DIFFRACTION4water.paramwater.top

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