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- PDB-5xoi: The structure of OsALKBH1 -

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Basic information

Entry
Database: PDB / ID: 5xoi
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
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
: / SUCCINIC 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
DepositionMay 28, 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)25,8793
Polymers25,7061
Non-polymers1732
Water2,630146
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 7.0)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-5 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.254, 67.633, 67.921
Angle α, β, γ (deg.)90.00, 99.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

21A-626-

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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#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.: 146 / 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: 44.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD(2-methyl-1,3-propanediol) , Tris base

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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: Apr 7, 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: 21158 / % possible obs: 96.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.059 / Net I/σ(I): 21.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.71 / CC1/2: 0.843 / Rpim(I) all: 0.246 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KHB

3khb


Resolution: 1.8→39.943 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.52
RfactorNum. reflection% reflection
Rfree0.2049 999 4.74 %
Rwork0.1807 --
obs0.1818 21058 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 9 146 1917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061809
X-RAY DIFFRACTIONf_angle_d0.892442
X-RAY DIFFRACTIONf_dihedral_angle_d4.0351095
X-RAY DIFFRACTIONf_chiral_restr0.062263
X-RAY DIFFRACTIONf_plane_restr0.006321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7857-1.87990.25881380.19992707X-RAY DIFFRACTION94
1.8799-1.99760.19791300.17772913X-RAY DIFFRACTION100
1.9976-2.15190.2411330.16672853X-RAY DIFFRACTION100
2.1519-2.36840.20131750.1682881X-RAY DIFFRACTION100
2.3684-2.7110.24361450.18242876X-RAY DIFFRACTION100
2.711-3.41530.18661200.18032910X-RAY DIFFRACTION99
3.4153-39.95290.18861580.18572919X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 33.8552 Å / Origin y: 32.2109 Å / Origin z: 16.9127 Å
111213212223313233
T0.157 Å20.0088 Å2-0.0043 Å2-0.1409 Å2-0.0099 Å2--0.1538 Å2
L0.8516 °20.1092 °20.0706 °2-0.2996 °2-0.075 °2--0.748 °2
S-0.0302 Å °-0.0457 Å °0.0648 Å °0.0001 Å °0.0073 Å °-0.0654 Å °-0.0396 Å °-0.0484 Å °-0 Å °
Refinement TLS groupSelection details: all

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