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- PDB-3bkz: X-ray structure of E coli AlkB crosslinked to dsDNA in the active site -

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Basic information

Entry
Database: PDB / ID: 3bkz
TitleX-ray structure of E coli AlkB crosslinked to dsDNA in the active site
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB
  • DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3')
  • DNA (5'-D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3')
KeywordsDNA REPAIR / OXIDOREDUCTASE/DNA / alkylation repair / protein DNA interaction / cross-linking / dioxygenase / OXIDOREDUCTASE-DNA COMPLEX
Function / homology
Function and homology information


oxidative RNA demethylation / DNA oxidative demethylase / oxidative DNA demethylase activity => GO:0035516 / oxidative DNA demethylase activity / oxidative single-stranded DNA demethylation / oxidative single-stranded RNA demethylation / DNA-N1-methyladenine dioxygenase activity / oxidative RNA demethylase activity / RNA repair / DNA dealkylation involved in DNA repair ...oxidative RNA demethylation / DNA oxidative demethylase / oxidative DNA demethylase activity => GO:0035516 / oxidative DNA demethylase activity / oxidative single-stranded DNA demethylation / oxidative single-stranded RNA demethylation / DNA-N1-methyladenine dioxygenase activity / oxidative RNA demethylase activity / RNA repair / DNA dealkylation involved in DNA repair / oxidative demethylation / DNA demethylation / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm
Similarity search - Function
Alkylated DNA repair protein AlkB / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Oxoglutarate/iron-dependent dioxygenase / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA (> 10) / 2-OXOGLUTARIC ACID / DNA / : / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsYi, C. / Yang, C.-G. / He, C.
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
DepositionDec 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 28, 2014Group: Non-polymer description / Structure summary
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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _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: Alpha-ketoglutarate-dependent dioxygenase alkB
B: DNA (5'-D(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3')
C: DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4735
Polymers30,2723
Non-polymers2012
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-11.8 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)41.397, 75.507, 46.788
Angle α, β, γ (deg.)90.00, 105.45, 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 / E.C.1.14.11.- / Alkylated DNA repair protein alkB


Mass: 22286.559 Da / Num. of mol.: 1 / Mutation: D135C
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(*DTP*DAP*DGP*DGP*DTP*DAP*DAP*DCP*DAP*DTP*DCP*DGP*DT)-3')


Mass: 4050.739 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*DAP*DAP*DCP*DGP*DAP*DTP*DAP*DTP*DTP*DAP*DCP*DCP*DT)-3')


Mass: 3934.599 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 294 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 / Α-Ketoglutaric acid


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


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 5000, 0.1M 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 500011
2NaClSodium chloride11
3MgCl211
4sodium Cacodylate11
5PEG 500012
6NaClSodium chloride12
7MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. all: 36607 / Num. obs: 36607 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHASESphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.664 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21236 1663 5 %RANDOM
Rwork0.18756 ---
obs0.18882 31663 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.876 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.13 Å2
2---0.4 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 529 11 292 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212556
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.042.3583641
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84822.83874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43415253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3541513
X-RAY DIFFRACTIONr_chiral_restr0.0610.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1720.2952
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21589
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0630.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3651.51052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5321649
X-RAY DIFFRACTIONr_scbond_it0.61831971
X-RAY DIFFRACTIONr_scangle_it0.9844.51992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 128 -
Rwork0.256 2264 -
obs--99.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3078-0.2984-0.39591.7020.16650.53520.02870.08120.0567-0.0678-0.01740.02760.0328-0.0164-0.0113-0.12710.0064-0.0067-0.13750.013-0.1617-8.2693-1.7559-21.3648
22.09430.1432-0.82660.0158-0.05290.32850.17890.5664-0.1057-0.2336-0.12890.1034-0.1182-0.0441-0.050.01160.0739-0.06380.0022-0.0167-0.0428-9.6532-17.5092-38.6714
39.24040.28334.8322.7612-0.04714.7752-0.25110.6292-0.0134-0.21190.23130.1444-0.2080.00520.0199-0.00650.048-0.00030.0140.036-0.0396-6.5317-19.9564-39.0628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC14 - 2141 - 201
2X-RAY DIFFRACTION2BA1 - 131 - 13
3X-RAY DIFFRACTION3CB1 - 131 - 13

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