[English] 日本語
Yorodumi
- PDB-8d6g: Nanorana parkeri saxiphilin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8d6g
TitleNanorana parkeri saxiphilin
ComponentsSaxiphilin
KeywordsANTITOXIN / Saxiphilin / Toxin resistance / Saxitoxin
Biological speciesNanorana parkeri (frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZakrzewska, S. / Chen, Z. / Minor, D.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)HDTRA-1-19-1-0040 United States
Department of Defense (DOD, United States)HDTRA-1-21-1-10011 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Definition of a saxitoxin (STX) binding code enables discovery and characterization of the anuran saxiphilin family.
Authors: Chen, Z. / Zakrzewska, S. / Hajare, H.S. / Alvarez-Buylla, A. / Abderemane-Ali, F. / Bogan, M. / Ramirez, D. / O'Connell, L.A. / Du Bois, J. / Minor Jr., D.L.
History
DepositionJun 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Saxiphilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1803
Polymers94,7041
Non-polymers4772
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-4 kcal/mol
Surface area36490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.046, 229.046, 67.428
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Saxiphilin


Mass: 94703.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanorana parkeri (frog) / Gene: XM_018555331.1 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20-25% v/v PEG400, 4-5% w/v PGA-LM, 100-200 mM sodium acetate, pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.2→43.29 Å / Num. obs: 66067 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 52.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05218 / Net I/σ(I): 12.66
Reflection shellResolution: 2.2→2.279 Å / Mean I/σ(I) obs: 0.89 / Num. unique obs: 6127 / CC1/2: 0.465

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O0D

6o0d


Resolution: 2.2→43.29 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 3252 4.92 %
Rwork0.1889 62787 -
obs0.1912 66039 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.49 Å2 / Biso mean: 66.1513 Å2 / Biso min: 30.04 Å2
Refinement stepCycle: final / Resolution: 2.2→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 54 229 6646
Biso mean--88.84 55.62 -
Num. residues----821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.36281230.3572524264790
2.23-2.270.38191060.34342552265892
2.27-2.30.35531120.31662641275395
2.31-2.340.3741600.29922658281897
2.34-2.390.35821500.2782753290399
2.39-2.430.31041350.263827752910100
2.43-2.480.26031420.251128032945100
2.48-2.540.31881480.243727272875100
2.54-2.60.31051360.240328092945100
2.6-2.660.3281640.248927192883100
2.66-2.730.3451510.25827352886100
2.73-2.810.32461580.245427712929100
2.81-2.90.25841610.237727502911100
2.9-3.010.26571140.24122727284199
3.01-3.130.29661350.22982783291899
3.13-3.270.27991330.220928022935100
3.27-3.440.25131770.215326992876100
3.44-3.660.251490.194327582907100
3.66-3.940.2121390.163927922931100
3.94-4.340.19621290.1432761289099
4.34-4.960.15121250.1312768289399
4.96-6.250.19481690.148927242893100
6.25-43.290.16881360.13872756289299

+
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