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- PDB-3o1m: Iron-Catalyzed Oxidation Intermediates Captured in A DNA Repair D... -

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Basic information

Entry
Database: PDB / ID: 3o1m
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*(ME6)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 / 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 / cytoplasm / cytosol
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: 1.75 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 1.2Jun 19, 2013Group: Database references
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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Structure summary / Category: 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(*T*AP*GP*GP*TP*AP*AP*(ME6)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)31,1645
Polymers30,9633
Non-polymers2012
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-12 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.440, 75.950, 51.170
Angle α, β, γ (deg.)90.00, 107.76, 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 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*(ME6)P*AP*CP*CP*GP*T)-3')


Mass: 4050.763 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is made using 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 sequence is made using solid-state DNA synthesizer.

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Non-polymers , 3 types, 331 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.: 329 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
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

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9266 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9266 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 47998 / Num. obs: 47806 / % possible obs: 99.6 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 19.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4763 / % possible all: 99.6

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Processing

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

3bie


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.744 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 6 / σ(I): 6 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19073 1531 5.1 %RANDOM
Rwork0.16599 ---
all0.1673 28902 --
obs0.16725 28324 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.917 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.11 Å2
2---0.38 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1571 501 11 329 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0212296
X-RAY DIFFRACTIONr_angle_refined_deg1.182.2583242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78622.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.79615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0481514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211616
X-RAY DIFFRACTIONr_mcbond_it0.4991.51039
X-RAY DIFFRACTIONr_mcangle_it0.9321679
X-RAY DIFFRACTIONr_scbond_it1.34231257
X-RAY DIFFRACTIONr_scangle_it2.1424.51558
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 96 -
Rwork0.192 1810 -
obs--85.28 %
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)
11.1764-0.1194-0.14661.56240.29350.30590.00420.00010.0419-0.071-0.00730.03070.00630.01490.00310.01840.00060.01630.02160.0167-0.0723-1.6950.61525.557
24.2804-1.3388-0.68652.02390.66710.30850.19120.6347-0.2192-0.3324-0.23080.1774-0.1349-0.06010.03960.09320.0428-0.00670.1138-0.0264-0.0499-1.321-14.7749.331
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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