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- PDB-5xeg: The structure of OsALKBH1 -

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Basic information

Entry
Database: PDB / ID: 5xeg
TitleThe structure of OsALKBH1
ComponentsOxidoreductase, 2OG-Fe oxygenase family protein, putative, expressed
KeywordsOXIDOREDUCTASE / OsALKBH1 Fe(II)- and-ketoglutarate-dependent dioxygenases
Function / homology
Function and homology information


dioxygenase activity / DNA repair / metal ion binding
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 superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Oxidoreductase, 2OG-Fe oxygenase family protein, putative, expressed
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, C. / Guo, Y. / Zeng, Z.
CitationJournal: Nat Plants / Year: 2018
Title: Identification and analysis of adenine N6-methylation sites in the rice genome.
Authors: Zhou, C. / Wang, C. / Liu, H. / Zhou, Q. / Liu, Q. / Guo, Y. / Peng, T. / Song, J. / Zhang, J. / Chen, L. / Zhao, Y. / Zeng, Z. / Zhou, D.X.
History
DepositionApr 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, 2OG-Fe oxygenase family protein, putative, expressed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9073
Polymers25,7061
Non-polymers2012
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The target protein was further purified by a Hitrap Q column(GEHealthcare) and a Superdex200 10/300 column (GE Healthcare) with buffer 150 mM NaCl, 20 mM Bis-tris(pH 6.8)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-4 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.150, 67.729, 67.967
Angle α, β, γ (deg.)90.00, 99.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21A-670-

HOH

31A-709-

HOH

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Components

#1: Protein Oxidoreductase, 2OG-Fe oxygenase family protein, putative, expressed


Mass: 25706.387 Da / Num. of mol.: 1 / Fragment: UNP residues 141-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: LOC_Os03g60190, OsJ_13105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10BI6
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


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


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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: MPD(2-methyl-1,3-propanediol), HEPES Sodium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20894 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.047 / Rsym value: 0.03 / Net I/σ(I): 32.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.6 / CC1/2: 0.965 / Rsym value: 0.106

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KHB

3khb


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.42 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20778 979 4.7 %RANDOM
Rwork0.16133 ---
obs0.16351 19808 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.393 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å2-0.02 Å2
2---0.01 Å2-0 Å2
3---1.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 11 210 1931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191756
X-RAY DIFFRACTIONr_bond_other_d0.0020.021698
X-RAY DIFFRACTIONr_angle_refined_deg2.0511.9912366
X-RAY DIFFRACTIONr_angle_other_deg1.10733928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97924.07976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79415310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4481511
X-RAY DIFFRACTIONr_chiral_restr0.1630.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211963
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02384
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_it2.0872.079873
X-RAY DIFFRACTIONr_mcbond_other1.9992.077872
X-RAY DIFFRACTIONr_mcangle_it2.5373.1021086
X-RAY DIFFRACTIONr_mcangle_other2.5373.1031087
X-RAY DIFFRACTIONr_scbond_it3.2892.479883
X-RAY DIFFRACTIONr_scbond_other3.2942.482879
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9893.5661277
X-RAY DIFFRACTIONr_long_range_B_refined7.33827.1692017
X-RAY DIFFRACTIONr_long_range_B_other7.34127.1672015
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 71 -
Rwork0.161 1399 -
obs--95.21 %

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