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- PDB-3o1o: Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair D... -

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Basic information

Entry
Database: PDB / ID: 3o1o
TitleIron-Catalyzed Oxidation Intermediates Captured in A DNA Repair Dioxygenase
Components
  • Alpha-ketoglutarate-dependent dioxygenase AlkB
  • DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3')
  • DNA (5'-D(*T*AP*GP*GP*TP*AP*AP*(MFT)P*AP*CP*CP*GP*T)-3')
KeywordsOXIDOREDUCTASE / Jelly-roll fold. / Demethylase
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 / DNA (> 10) / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsYi, C. / Jia, G. / Hou, G. / Dai, Q. / Zhang, W. / Zheng, G. / Jian, X. / Yang, C.-G. / Cui, Q. / He, C.
CitationJournal: Nature / Year: 2010
Title: Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase
Authors: Yi, C. / Jia, G. / Hou, G. / Dai, Q. / Zhang, W. / Zheng, G. / Jian, X. / Yang, C.-G. / Cui, Q. / He, C.
History
DepositionJul 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references / Structure summary
Revision 1.3May 28, 2014Group: Non-polymer description / Structure summary
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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(*T*AP*GP*GP*TP*AP*AP*(MFT)P*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1785
Polymers30,9773
Non-polymers2012
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-16 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.380, 75.930, 51.790
Angle α, β, γ (deg.)90.00, 108.32, 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: 22961.303 Da / Num. of mol.: 1
Fragment: N-terminus 11 amino acids truncated AlkB (UNP residues 12 to 216)
Mutation: S129C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: alkB, aidD, b2212, JW2200 / Production host: Escherichia coli (E. coli) / Strain (production host): D3-157
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(*T*AP*GP*GP*TP*AP*AP*(MFT)P*AP*CP*CP*GP*T)-3')


Mass: 4064.767 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This is made with solid-state DNA synthesizer.
#3: DNA chain DNA (5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3')


Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This is made with solid-state DNA synthesizer.

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Non-polymers , 3 types, 250 molecules

#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
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

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9266 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 9, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9266 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 29870 / Num. obs: 28228 / % possible obs: 94.5 % / Observed criterion σ(F): 2.3 / Observed criterion σ(I): 2.3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.401
Reflection shellResolution: 1.75→1.82 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.3 / % possible all: 71.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0073refinement
HKL-2000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BIE

3bie


Resolution: 1.92→15 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.934 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 4 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22223 1082 4.8 %RANDOM
Rwork0.17446 ---
all0.177 22091 --
obs0.17674 21307 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.28 Å2
2---0.41 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.92→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 502 11 248 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212260
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3292.2663187
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74822.89576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11515254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3311513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6011.51019
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07821639
X-RAY DIFFRACTIONr_scbond_it1.5431241
X-RAY DIFFRACTIONr_scangle_it2.344.51546
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 67 -
Rwork0.206 1381 -
obs--85.83 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3433-0.0466-0.131.40430.33210.4341-0.0055-0.01470.0767-0.06810.00120.02790.00010.00380.00430.0039-0.00030.01280.01630.0169-0.0205-1.890.88325.416
24.7092-1.1357-0.77352.40010.58440.38460.23040.7279-0.1457-0.3605-0.20610.2633-0.1203-0.0678-0.02430.08480.0478-0.02370.1247-0.00690.0119-1.428-14.4919.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 214
2X-RAY DIFFRACTION2B2 - 13
3X-RAY DIFFRACTION2C1 - 13

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