[English] 日本語
Yorodumi
- PDB-6avd: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6avd
TitleExploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
ComponentsPotassium channel toxin alpha-KTx 6.9
KeywordsTOXIN / Knottins / Cystine knot / Toxins
Function / homology
Function and homology information


ion channel inhibitor activity / potassium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Scorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium channel toxin alpha-KTx 6.9
Similarity search - Component
Biological speciesOpistophthalmus carinatus (scorpion)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsGewe, M.M. / Rupert, P. / Strong, R.K.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Screening, large-scale production and structure-based classification of cystine-dense peptides.
Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K.
History
DepositionSep 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Potassium channel toxin alpha-KTx 6.9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3802
Polymers4,2841
Non-polymers961
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)21.502, 26.209, 31.102
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide Potassium channel toxin alpha-KTx 6.9 / OcKTx4


Mass: 4284.128 Da / Num. of mol.: 1 / Fragment: residues 24-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Opistophthalmus carinatus (scorpion) / Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q6XLL6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.02 Å3/Da / Density % sol: 39.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM Na Acetate pH 4.5, 200 mM Li2SO4, 50% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 2751 / % possible obs: 83.9 % / Redundancy: 1.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.045 / Χ2: 1.981 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.8 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 108 / CC1/2: 0.944 / Rpim(I) all: 0.092 / Χ2: 1.981 / % possible all: 67.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→30.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.593 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20506 125 4.5 %RANDOM
Rwork0.13905 ---
obs0.14215 2623 83.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20.13 Å2
2---0.34 Å20 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms289 0 5 57 351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019299
X-RAY DIFFRACTIONr_bond_other_d0.0040.02275
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.997401
X-RAY DIFFRACTIONr_angle_other_deg0.8113644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.968539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.79223.3339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9791556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.528152
X-RAY DIFFRACTIONr_chiral_restr0.1340.244
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0254
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3561.058159
X-RAY DIFFRACTIONr_mcbond_other1.271.049158
X-RAY DIFFRACTIONr_mcangle_it2.0331.752197
X-RAY DIFFRACTIONr_mcangle_other2.031.76198
X-RAY DIFFRACTIONr_scbond_it4.3491.527140
X-RAY DIFFRACTIONr_scbond_other2.1931.458137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4552.218199
X-RAY DIFFRACTIONr_long_range_B_refined8.34612.492340
X-RAY DIFFRACTIONr_long_range_B_other7.52710.665322
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 5 -
Rwork0.166 159 -
obs--66.94 %
Refinement TLS params.Method: refined / Origin x: 19.4634 Å / Origin y: 4.3833 Å / Origin z: 4.176 Å
111213212223313233
T0.0022 Å20.0001 Å2-0.0058 Å2-0.0027 Å2-0.0003 Å2--0.0355 Å2
L2.542 °2-0.5288 °2-0.7837 °2-2.1333 °20.044 °2--2.5538 °2
S-0.0281 Å °-0.0187 Å °0.0607 Å °0.0228 Å °0.0121 Å °0.0636 Å °0.0394 Å °0.0031 Å °0.0161 Å °

+
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