[English] 日本語
Yorodumi
- PDB-5y8f: Crystal Structure of a prokaryotic SEFIR domain -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more