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- PDB-3i49: Crystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate ... -

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Basic information

Entry
Database: PDB / ID: 3i49
TitleCrystal Structure of AlkB in complex with Fe(II), 2-oxoglutarate and methylated trinucleotide T-meC-T
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB
  • DNA (5'-D(P*TP*(ME6)P*T)-3')
KeywordsOXIDOREDUCTASE/DNA / beta jellyroll / protein-DNA complex / Dioxygenase / 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 / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation 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 / 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 / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsYu, B. / Hunt, J.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Enzymological and structural studies of the mechanism of promiscuous substrate recognition by the oxidative DNA repair enzyme AlkB.
Authors: Yu, B. / Hunt, J.F.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB
B: DNA (5'-D(P*TP*(ME6)P*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6814
Polymers24,4792
Non-polymers2022
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-21 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.374, 41.374, 117.213
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 23610.975 Da / Num. of mol.: 1 / Fragment: UNP residues 12-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: aidD, alkB, b2212, JW2200 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / 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
#2: DNA chain DNA (5'-D(P*TP*(ME6)P*T)-3')


Mass: 867.645 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97947 Å
DetectorDetector: CCD / Date: Nov 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 25984 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.074 / Χ2: 1.081 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.638.20.65612890.8431100
1.63-1.668.20.56813530.8681100
1.66-1.698.20.48212340.9031100
1.69-1.7280.44413370.9381100
1.72-1.768.10.36912550.9361100
1.76-1.88.30.32613240.9511100
1.8-1.858.30.2712590.9861100
1.85-1.97.60.22613101.0741100
1.9-1.955.80.2312871.596199.4
1.95-2.028.10.15213081.1081100
2.02-2.097.30.13612981.1811100
2.09-2.178.10.11413101.1141100
2.17-2.277.10.10612791.3091100
2.27-2.398.30.0912801.2311100
2.39-2.548.40.08413121.251100
2.54-2.7480.07313111.255199.8
2.74-3.018.40.05912861.2671100
3.01-3.458.10.04613381.216199.9
3.45-4.347.20.03612821.1199.8
4.34-508.40.02713320.731199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.2 / Cor.coef. Fo:Fc: 62.48
Highest resolutionLowest resolution
Rotation4 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMO1.2phasing
CNS1.2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.8 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.882 / Data cutoff high absF: 1210185 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2550 10.3 %RANDOM
Rwork0.186 ---
obs-24783 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.471 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 147.6 Å2 / Biso mean: 20.706 Å2 / Biso min: 7.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 61 11 281 1917
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 355 9.4 %
Rwork0.222 3439 -
all-3794 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.param_bywater.top
X-RAY DIFFRACTION3water_rep.paramdna-rna.top_by
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5akg.parakg.top

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