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- PDB-3bi3: X-ray structure of AlkB protein bound to dsDNA containing 1meA/A ... -

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Basic information

Entry
Database: PDB / ID: 3bi3
TitleX-ray structure of AlkB protein bound to dsDNA containing 1meA/A with cofactors
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB
  • DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3')
  • DNA (5'-D(*TP*AP*GP*GP*TP*AP*AP*(MA7)P*AP*(2YR)P*CP*GP*T)-3')
KeywordsOxidoreductase/DNA / Dioxygenase / protein DNA interaction / alkylation repair / DNA damage / DNA repair / Iron / Metal-binding / Oxidoreductase / Oxidoreductase-DNA COMPLEX
Function / homology
Function and homology information


response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding / DNA repair / cytosol / cytoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / DNA / DNA (> 10) / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYi, C. / Yang, C.-G.
CitationJournal: Nature / Year: 2008
Title: Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Authors: Yang, C.G. / Yi, C. / Duguid, E.M. / Sullivan, C.T. / Jian, X. / Rice, P.A. / He, C.
History
DepositionNov 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 21, 2014Group: Other
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB
B: DNA (5'-D(*TP*AP*GP*GP*TP*AP*AP*(MA7)P*AP*(2YR)P*CP*GP*T)-3')
C: DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5415
Polymers30,3403
Non-polymers2012
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.407, 75.629, 50.972
Angle α, β, γ (deg.)90.00, 107.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB / Alkylated DNA repair protein alkB


Mass: 22314.504 Da / Num. of mol.: 1 / Fragment: catalytic repair domain / Mutation: S129C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: alkB, aidD / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P05050, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*TP*AP*GP*GP*TP*AP*AP*(MA7)P*AP*(2YR)P*CP*GP*T)-3')


Mass: 4074.788 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*DAP*DAP*DCP*DGP*DGP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3')


Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 170 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% (w/v) PEG 8K, 100 mM Sodium Chloride, 25 mM magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 8K11
2Sodium Chloride11
3magnesium chloride11
4cacodylate11
5PEG 8K12
6Sodium Chloride12
7magnesium chloride12
8cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 24645 / Num. obs: 24645 / % possible obs: 89.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / % possible all: 69.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.117 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24714 1114 5.1 %RANDOM
Rwork0.21462 ---
obs0.21634 20726 92.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.669 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å2-0.08 Å2
2---2.55 Å20 Å2
3---4.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 515 11 168 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212247
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0932.2543163
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6515208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25723.03879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08915257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3161514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021605
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1750.2937
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21420
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.090.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2791.51057
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45921661
X-RAY DIFFRACTIONr_scbond_it0.64331532
X-RAY DIFFRACTIONr_scangle_it1.154.51502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 65 -
Rwork0.235 1263 -
obs--78.49 %
Refinement TLS params.Method: refined / Origin x: -6.5917 Å / Origin y: 1.7121 Å / Origin z: -23.2903 Å
111213212223313233
T-0.1581 Å2-0.0012 Å2-0.0212 Å2--0.1479 Å20.0171 Å2---0.1743 Å2
L2.2419 °2-0.1061 °2-0.3796 °2-2.597 °20.4873 °2--0.5785 °2
S-0.0304 Å °0.056 Å °0.1167 Å °-0.1516 Å °0.0229 Å °0.0618 Å °-0.029 Å °0.0066 Å °0.0075 Å °

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