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- PDB-5y8e: Crystal Structure of a prokaryotic SEFIR domain -

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Basic information

Entry
Database: PDB / ID: 5y8e
TitleCrystal Structure of a prokaryotic SEFIR domain
ComponentsSefir domain protein
KeywordsSIGNALING PROTEIN / SEFIR
Function / homologySEFIR domain / SEFIR domain profile. / NAD catabolic process / TIR domain / NAD+ nucleosidase activity / 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 / SYNCHROTRON / MAD / Resolution: 1.804 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sefir domain protein


Theoretical massNumber of molelcules
Total (without water)18,0421
Polymers18,0421
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9030 Å2
Unit cell
Length a, b, c (Å)38.739, 61.673, 39.272
Angle α, β, γ (deg.)90.00, 115.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sefir domain protein


Mass: 18042.453 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 8-160
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.: 221 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / 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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→35.33 Å / Num. obs: 108121 / % possible obs: 99.4 % / Redundancy: 4.1 % / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.804→35.327 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.1963 765 5.01 %
Rwork0.1668 --
obs0.1683 15269 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.804→35.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 0 221 1489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061316
X-RAY DIFFRACTIONf_angle_d0.9631785
X-RAY DIFFRACTIONf_dihedral_angle_d14.539493
X-RAY DIFFRACTIONf_chiral_restr0.069187
X-RAY DIFFRACTIONf_plane_restr0.004229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8036-1.94290.23151320.17122872X-RAY DIFFRACTION98
1.9429-2.13840.20431520.16122891X-RAY DIFFRACTION100
2.1384-2.44770.23461710.17132901X-RAY DIFFRACTION100
2.4477-3.08360.19361590.17712886X-RAY DIFFRACTION100
3.0836-35.33390.17311510.16032954X-RAY DIFFRACTION99
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)
11.69130.04590.06442.59990.31931.51180.1121-0.1359-0.16280.2046-0.0418-0.06370.14570.1511-0.06560.09180.0136-0.01060.1083-0.00950.102616.636832.223813.9414
21.85751.0496-0.34012.2087-0.91880.6860.0897-0.1945-0.04590.3764-0.13460.0848-0.14250.0447-0.01880.1501-0.0118-0.02140.10470.00680.097310.565730.935119.6864
31.04160.31270.38186.6137-0.01921.0394-0.03320.118-0.0554-0.44530.15340.4935-0.0471-0.0313-0.10680.1186-0.00290.03130.1480.02220.20010.521329.624914.264
42.06990.0774-0.05361.7383-0.22322.0778-0.02360.3515-0.2381-0.2084-0.08580.07320.3602-0.18190.03020.1485-0.00880.01590.162-0.03670.10269.292132.13513.0689
52.29510.7356-0.08421.7165-0.51323.57940.13750.1751-1.2571-0.43730.0568-0.08771.28740.2350.09410.393-0.0138-0.04950.2592-0.04830.47921.261324.57514.3396
63.88031.06730.48510.7572-0.14310.45090.00530.41560.30280.0160.04040.1447-0.0203-0.0613-0.03570.11210.01320.00020.14690.01460.14262.981640.12334.8499
71.66380.69640.45330.77670.1620.7653-0.18510.52130.0634-0.31880.1838-0.0146-0.1775-0.09520.00080.19250.01410.00970.27590.01080.123614.87237.6296-2.3215
83.9069-1.2641-1.59091.94830.82032.25640.0802-0.08050.3484-0.0859-0.036-0.137-0.31970.1324-0.0730.1451-0.02980.00680.0976-0.01540.106119.915845.590210.2341
90.6506-1.3581-0.04473.38550.04490.00770.07020.64250.0826-0.4883-0.272-0.2288-0.6057-0.56060.09010.35510.0901-0.00810.2944-0.04520.22555.908455.993810.752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:29)
2X-RAY DIFFRACTION2chain 'A' and (resseq 30:42)
3X-RAY DIFFRACTION3chain 'A' and (resseq 43:56)
4X-RAY DIFFRACTION4chain 'A' and (resseq 57:74)
5X-RAY DIFFRACTION5chain 'A' and (resseq 75:87)
6X-RAY DIFFRACTION6chain 'A' and (resseq 88:103)
7X-RAY DIFFRACTION7chain 'A' and (resseq 104:129)
8X-RAY DIFFRACTION8chain 'A' and (resseq 130:142)
9X-RAY DIFFRACTION9chain 'A' and (resseq 143:150)

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