[English] 日本語
Yorodumi
- PDB-3era: RECOMBINANT ERABUTOXIN A (S8T MUTANT) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3era
TitleRECOMBINANT ERABUTOXIN A (S8T MUTANT)
ComponentsERABUTOXIN A
KeywordsNEUROTOXIN / SNAKE NEUROTOXIN / VENOM / POSTSYNAPTIC NEUROTOXIN
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 toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
THIOCYANATE ION / Erabutoxin a
Similarity search - Component
Biological speciesLaticauda semifasciata (broad-banded blue sea krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR / Resolution: 1.7 Å
AuthorsGaucher, J.F. / Menez, R. / Arnoux, B. / Menez, A. / Ducruix, A.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: High resolution x-ray analysis of two mutants of a curaremimetic snake toxin
Authors: Gaucher, J.F. / Menez, R. / Arnoux, B. / Menez, A. / Ducruix, A.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Genetic Engineering of Snake Toxins. The Functional Site of Erabutoxin A, as Delineated by Site-Directed Mutagenesis, Includes Variant Residues
Authors: Tremeau, O. / Lemaire, C. / Drevet, P. / Pinkasfeld, S. / Ducancel, F. / Boulain, J.C. / Menez, A.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Genetic Engineering of Snake Toxins. Role of Invariant Residues in the Structural and Functional Properties of a Curaremimetic Toxin, as Probed by Site-Directed Mutagenesis
Authors: Pillet, L. / Tremeau, O. / Ducancel, F. / Drevet, P. / Zinn-Justin, S. / Pinkasfeld, S. / Boulain, J.C. / Menez, A.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of a Dimeric Form of Erabutoxin-B, Crystallized from Thiocyanate Solution
Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A.
#4: Journal: J.Biol.Chem. / Year: 1989
Title: The Crystal Structure of Erabutoxin a at 2.0-A Resolution
Authors: Corfield, P.W. / Lee, T.J. / Low, B.W.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1988
Title: Refinement at 1.4 A Resolution of a Model of Erabutoxin B: Treatment of Ordered Solvent and Discrete Disorder
Authors: Smith, J.L. / Corfield, P.W.R. / Hendrickson, W.A. / Low, B.W.
History
DepositionJun 25, 1997Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ERABUTOXIN A
B: ERABUTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9105
Polymers13,7352
Non-polymers1743
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.418, 53.013, 40.467
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: (-0.99975, -0.00367, 0.02204), (0.01952, 0.33621, 0.94158), (-0.01087, 0.94178, -0.33606)
Vector: 47.12906, 25.64156, -36.72058)

-
Components

#1: Protein ERABUTOXIN A


Mass: 6867.741 Da / Num. of mol.: 2 / Mutation: S8T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Laticauda semifasciata (broad-banded blue sea krait)
Plasmid: PEZZ 18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB 101 / References: UniProt: P60775
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: CRYSTALLIZATION WERE PERFORMED AT 291K BY THE HANGING DROP METHOD. DROPS OF 2 MICROLITRE OF 0.007M PROTEIN AND 2 MICROLITRE OF RESERVOIR WERE EQUILIBRATED AGAINST 0.32M NASCN, 0.05M NAOAC ...Details: CRYSTALLIZATION WERE PERFORMED AT 291K BY THE HANGING DROP METHOD. DROPS OF 2 MICROLITRE OF 0.007M PROTEIN AND 2 MICROLITRE OF RESERVOIR WERE EQUILIBRATED AGAINST 0.32M NASCN, 0.05M NAOAC BUFFER SOLUTION (PH 4.5), vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mMtoxin1drop
2210 mM1reservoirNaSCN
350 mM1reservoirNaOAc

-
Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 1.7→13.9 Å / Num. obs: 13459 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 3.4 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 9.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.29 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 13852 / % possible obs: 97.8 % / Num. measured all: 46741 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 3.4

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAAGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR
Starting model: STRUCTURE OF RECOMBINANT ERABUTOXIN A (S8G MUTANT)

Resolution: 1.7→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: AT THE END OF REFINEMENT RFREE DATA SET WAS COMBINED WITH OTHER DATA FOR THE LAST STEP OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1243 9.9 %RANDOM
Rwork0.179 ---
obs0.179 12566 96.9 %-
Displacement parametersBiso mean: 15.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.18 Å
Luzzati d res low-10 Å
Luzzati sigma a-0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 9 116 1083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.95
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.29
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.251 125 9.1 %
Rwork0.24 1248 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.95
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.24

+
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