[English] 日本語
Yorodumi
- PDB-1qkd: ERABUTOXIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qkd
TitleERABUTOXIN
ComponentsERABUTOXIN A
KeywordsNEUROTOXIN / ERABUTOXIN
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesLaticauda semifasciata (broad-banded blue sea krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsNastopoulos, V. / Kanellopoulos, P.N. / Tsernoglou, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of dimeric and monomeric erabutoxin a refined at 1.5 A resolution.
Authors: Nastopoulos, V. / Kanellopoulos, P.N. / Tsernoglou, D.
History
DepositionJan 16, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ERABUTOXIN A
B: ERABUTOXIN A


Theoretical massNumber of molelcules
Total (without water)13,7072
Polymers13,7072
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.320, 53.540, 40.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.998, -0.0264, -0.0579), (-0.0635, 0.3626, 0.9298), (-0.0035, 0.9316, -0.3635)
Vector: 48.3697, -8.311, 14.5737)

-
Components

#1: Protein ERABUTOXIN A


Mass: 6853.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: JAPANESE SEA SNAKE
Source: (natural) Laticauda semifasciata (broad-banded blue sea krait)
Secretion: VENOM / References: UniProt: P60775
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
240 %satammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.49→17.4 Å / Num. obs: 19420 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.065 / Net I/σ(I): 29.7
Reflection shellResolution: 1.49→1.6 Å / Redundancy: 14 % / Mean I/σ(I) obs: 5.25 / Rsym value: 0.204 / % possible all: 86
Reflection
*PLUS
Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 86 % / Rmerge(I) obs: 0.204

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EBX

6ebx


Resolution: 1.49→17.4 Å / σ(F): 0 / Details: X-PLOR WAS ALSO USED
RfactorNum. reflection% reflection
all0.169 --
obs-19420 100 %
Refinement stepCycle: LAST / Resolution: 1.49→17.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 206 1193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.17
X-RAY DIFFRACTIONt_dihedral_angle_d18.13
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005
X-RAY DIFFRACTIONt_gen_planes0.013
X-RAY DIFFRACTIONt_it7.22
X-RAY DIFFRACTIONt_nbd0.04
Software
*PLUS
Name: TNT / Version: 5EA / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.13
X-RAY DIFFRACTIONt_plane_restr0.013

+
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