[English] 日本語
Yorodumi
- PDB-6o0d: Saxiphilin Apo structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o0d
TitleSaxiphilin Apo structure
ComponentsSaxiphilin
KeywordsANTITOXIN / saxitoxin / paralytic shellfish poisoning
Function / homology
Function and homology information


recycling endosome / iron ion transport / antibacterial humoral response / early endosome / extracellular space / plasma membrane
Similarity search - Function
Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin
Similarity search - Domain/homology
Biological speciesLithobates catesbeiana (American bullfrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYen, T.J. / Lolicato, M. / Minor, D.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL080050 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117263-01A1 United States
CitationJournal: Sci Adv / Year: 2019
Title: Structure of the saxiphilin:saxitoxin (STX) complex reveals a convergent molecular recognition strategy for paralytic toxins.
Authors: Yen, T.J. / Lolicato, M. / Thomas-Tran, R. / Du Bois, J. / Minor Jr., D.L.
History
DepositionFeb 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Saxiphilin
B: Saxiphilin


Theoretical massNumber of molelcules
Total (without water)188,4572
Polymers188,4572
Non-polymers00
Water2,630146
1
A: Saxiphilin


Theoretical massNumber of molelcules
Total (without water)94,2281
Polymers94,2281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Saxiphilin


Theoretical massNumber of molelcules
Total (without water)94,2281
Polymers94,2281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.158, 111.309, 254.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Saxiphilin / SAX


Mass: 94228.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lithobates catesbeiana (American bullfrog)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P31226
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate pH 6.5, 5% PEG 8000, and 40% 2-methyl-2,4-pentanediol (MPD)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.5→48.17 Å / Num. obs: 95358 / % possible obs: 99.77 % / Redundancy: 12 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.54 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
Aimless0.5.32data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.168 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 4734 4.98 %
Rwork0.2243 --
obs0.2257 95117 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12559 0 0 146 12705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312849
X-RAY DIFFRACTIONf_angle_d0.67817365
X-RAY DIFFRACTIONf_dihedral_angle_d14.6227938
X-RAY DIFFRACTIONf_chiral_restr0.0431887
X-RAY DIFFRACTIONf_plane_restr0.0042247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.45491350.42132917X-RAY DIFFRACTION96
2.5284-2.55820.43021580.40362889X-RAY DIFFRACTION99
2.5582-2.58930.41611370.38533010X-RAY DIFFRACTION100
2.5893-2.62210.42441580.36392979X-RAY DIFFRACTION100
2.6221-2.65660.40211510.34122956X-RAY DIFFRACTION100
2.6566-2.6930.38391550.31462987X-RAY DIFFRACTION100
2.693-2.73150.31221410.28543010X-RAY DIFFRACTION100
2.7315-2.77220.3461460.28093000X-RAY DIFFRACTION100
2.7722-2.81560.34811590.27622974X-RAY DIFFRACTION100
2.8156-2.86170.31231710.2822974X-RAY DIFFRACTION100
2.8617-2.91110.3431550.27762998X-RAY DIFFRACTION100
2.9111-2.9640.39221590.29962981X-RAY DIFFRACTION100
2.964-3.0210.32111700.2742980X-RAY DIFFRACTION100
3.021-3.08260.29451720.26932991X-RAY DIFFRACTION100
3.0826-3.14970.29491420.25632984X-RAY DIFFRACTION100
3.1497-3.22290.27821750.24163022X-RAY DIFFRACTION100
3.2229-3.30350.27191650.24552976X-RAY DIFFRACTION100
3.3035-3.39280.27521620.23132999X-RAY DIFFRACTION100
3.3928-3.49260.26411650.23623006X-RAY DIFFRACTION100
3.4926-3.60530.31961610.24063016X-RAY DIFFRACTION100
3.6053-3.73410.23581720.22192995X-RAY DIFFRACTION100
3.7341-3.88350.26971520.21123033X-RAY DIFFRACTION100
3.8835-4.06020.2481430.19373032X-RAY DIFFRACTION100
4.0602-4.27410.21591500.19493071X-RAY DIFFRACTION100
4.2741-4.54170.20491470.18973027X-RAY DIFFRACTION100
4.5417-4.89210.21521490.19073078X-RAY DIFFRACTION100
4.8921-5.38380.21221580.1983053X-RAY DIFFRACTION100
5.3838-6.16150.24821760.22463089X-RAY DIFFRACTION100
6.1615-7.75760.22311800.22543090X-RAY DIFFRACTION100
7.7576-48.17720.17711700.17183266X-RAY DIFFRACTION100

+
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://pdbjlvh1.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