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- PDB-5y8f: Crystal Structure of a prokaryotic SEFIR domain -

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Basic information

Entry
Database: PDB / ID: 5y8f
TitleCrystal Structure of a prokaryotic SEFIR domain
ComponentsSefir domain protein
KeywordsSIGNALING PROTEIN / SEFIR
Function / homologySEFIR domain / SEFIR domain profile. / NAD+ catabolic process / NAD+ nucleosidase activity / TIR domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / signal transduction / Sefir domain protein
Function and homology information
Biological speciesBacillus cereus F65185 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, R. / Ye, S. / Zhu, Y. / Yang, H.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structure of a prokaryotic SEFIR domain reveals two novel SEFIR-SEFIR interaction modes.
Authors: Yang, H. / Zhu, Y. / Chen, X. / Li, X. / Ye, S. / Zhang, R.
History
DepositionAug 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sefir domain protein
B: Sefir domain protein


Theoretical massNumber of molelcules
Total (without water)33,9062
Polymers33,9062
Non-polymers00
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-3 kcal/mol
Surface area13890 Å2
Unit cell
Length a, b, c (Å)37.860, 68.017, 54.941
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sefir domain protein


Mass: 16953.119 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 8-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus F65185 (bacteria) / Gene: bcere0025_60270 / Production host: Escherichia coli (E. coli) / References: UniProt: C2XMK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 0.1 M imidozale pH 8.0, 30% PEG 8000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29.18 Å / Num. obs: 271348 / % possible obs: 94.9 % / Redundancy: 2.8 % / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.177 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.29
RfactorNum. reflection% reflection
Rfree0.2219 917 5.14 %
Rwork0.1857 --
obs0.1875 17854 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 0 346 2738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042462
X-RAY DIFFRACTIONf_angle_d0.9823328
X-RAY DIFFRACTIONf_dihedral_angle_d8.6862044
X-RAY DIFFRACTIONf_chiral_restr0.055344
X-RAY DIFFRACTIONf_plane_restr0.006426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9967-2.10190.292970.23451869X-RAY DIFFRACTION73
2.1019-2.23350.26641450.21572433X-RAY DIFFRACTION97
2.2335-2.40590.24761170.21292560X-RAY DIFFRACTION100
2.4059-2.64790.25621550.2162512X-RAY DIFFRACTION100
2.6479-3.03070.25211230.21012528X-RAY DIFFRACTION99
3.0307-3.8170.20331400.16372541X-RAY DIFFRACTION99
3.817-29.18010.17531400.15252494X-RAY DIFFRACTION96

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