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- PDB-5ylb: Crystal structure of Ofd2 from Schizosaccharomyces pombe at 1.80 A -

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Basic information

Entry
Database: PDB / ID: 5ylb
TitleCrystal structure of Ofd2 from Schizosaccharomyces pombe at 1.80 A
ComponentsUncharacterized protein P8A3.02c
KeywordsOXIDOREDUCTASE / beta barrel
Function / homology
Function and homology information


regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / ferrous iron binding / histone binding / cellular response to hypoxia / mitochondrial matrix / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II ...regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / ferrous iron binding / histone binding / cellular response to hypoxia / mitochondrial matrix / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Alpha-ketoglutarate-dependent dioxygenase alkB homologue 7 / 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
: / Uncharacterized protein P8A3.02c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWang, J. / Gao, Y.X. / Guo, G.R. / Zhu, Z.L. / Teng, M.K. / Niu, L.W.
Funding support China, 4items
OrganizationGrant numberCountry
Chinese Ministry of Science and Technology2012CB917200 China
Chinese Ministry of Science and Technology2011CBA00800 China
Chinese National Natural Science Foundation31130018 China
Chinese National Natural Science Foundation31170726 China
CitationJournal: to be published
Title: Crystal structure of Ofd2 from Schizosaccharomyces pombe at 1.80 A
Authors: Wang, J. / Gao, Y.X. / Guo, G.R. / Teng, M.K. / Niu, L.W.
History
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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: Uncharacterized protein P8A3.02c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7232
Polymers21,6671
Non-polymers561
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area9700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.506, 80.386, 81.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21A-460-

HOH

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Components

#1: Protein Uncharacterized protein P8A3.02c / 2OG(2-oxoglutarate)-iron(Fe(II)) dependent dioxygenase Ofd2


Mass: 21666.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: SPAP8A3.02c
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9UT12
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18% MPEG 5000, 0.1M HEPES,pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.79→57.4 Å / Num. obs: 20695 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 2.69

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3THP

3thp


Resolution: 1.79→57.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.906 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.12
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1123 5.1 %RANDOM
Rwork0.1853 ---
obs0.1876 20695 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.94 Å2 / Biso mean: 33.226 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å2-0 Å2-0 Å2
2---3.6 Å20 Å2
3---1.29 Å2
Refinement stepCycle: final / Resolution: 1.79→57.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 1 132 1643
Biso mean--25.77 39 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191551
X-RAY DIFFRACTIONr_bond_other_d0.0010.021462
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9482104
X-RAY DIFFRACTIONr_angle_other_deg0.63433364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9875186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34623.97373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35715265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.007159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02368
LS refinement shellResolution: 1.795→1.841 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 76 -
Rwork0.273 1417 -
all-1493 -
obs--93.37 %

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