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- PDB-3i3q: Crystal Structure of AlkB in complex with Mn(II) and 2-oxoglutarate -

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Basic information

Entry
Database: PDB / ID: 3i3q
TitleCrystal Structure of AlkB in complex with Mn(II) and 2-oxoglutarate
ComponentsAlpha-ketoglutarate-dependent dioxygenase alkB
KeywordsOXIDOREDUCTASE / beta jellyroll / Dioxygenase / DNA damage / DNA repair / Iron / Metal-binding
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 / : / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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
DepositionJun 30, 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
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_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

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB
B: Alpha-ketoglutarate-dependent dioxygenase alkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6246
Polymers47,2222
Non-polymers4024
Water6,053336
1
A: Alpha-ketoglutarate-dependent dioxygenase alkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8123
Polymers23,6111
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-ketoglutarate-dependent dioxygenase alkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8123
Polymers23,6111
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.746, 39.187, 72.407
Angle α, β, γ (deg.)77.18, 74.80, 63.62
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 23610.975 Da / Num. of mol.: 2 / 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: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 42 %
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: 1.4→50 Å / Num. obs: 71196 / % possible obs: 96.1 % / Redundancy: 4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.4-1.4240.59193.6
1.42-1.4540.483193.8
1.45-1.4840.416194.2
1.48-1.5140.344194.6
1.51-1.543.90.289194.5
1.54-1.5840.239194.9
1.58-1.6240.195195.1
1.62-1.6640.169195.2
1.66-1.7140.149195.6
1.71-1.7640.123196
1.76-1.8340.101196.2
1.83-1.940.081196.4
1.9-1.9940.073196.7
1.99-2.093.90.06196.9
2.09-2.2240.048197.4
2.22-2.393.90.045197.7
2.39-2.6340.04198
2.63-3.0240.034198.3
3.02-3.83.90.029198.9
3.8-503.80.026198.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.3 / Cor.coef. Fo:Fc: 40.13
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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→32.97 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.2 / Data cutoff high absF: 792490.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.207 6847 9.9 %RANDOM
Rwork0.182 ---
obs0.182 69181 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8179 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å23.03 Å2-0.17 Å2
2---0.86 Å22.26 Å2
3----2.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.4→32.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 22 336 3536
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.742.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 1083 10.1 %
Rwork0.246 9653 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4akg.parakg.top

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