[English] 日本語
Yorodumi
- PDB-6imf: Crystal structure of TOXIN/ANTITOXIN complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6imf
TitleCrystal structure of TOXIN/ANTITOXIN complex
Components
  • Cysteine-rich venom protein triflin
  • Small serum protein 2
KeywordsTOXIN/ANTITOXIN / COMPLEX / ANTITOXIN / TOXIN-ANTITOXIN COMPLEX / TOXIN
Function / homology
Function and homology information


calcium channel regulator activity / toxin activity / extracellular space / extracellular region
Similarity search - Function
Beta-microseminoprotein / Beta-microseminoprotein (PSP-94) / Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site ...Beta-microseminoprotein / Beta-microseminoprotein (PSP-94) / Crisp domain / Cysteine-rich secretory protein / Cysteine-rich secretory protein, SCP domain / Crisp-like domain / Crisp / Venom allergen 5-like / CRISP family signature 2. / Allergen V5/Tpx-1-related, conserved site / CRISP family signature 1. / Cysteine-rich secretory protein-related / ShKT domain / ShKT domain profile. / Pathogenesis-related Protein p14a / CAP / SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Small serum protein 2 / Cysteine-rich venom protein triflin
Similarity search - Component
Biological speciesProtobothrops flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShioi, N. / Tadokoro, T. / Shioi, S. / Hu, Y. / Kurahara, L.H. / Okabe, Y. / Matsubara, H. / Kita, S. / Ose, T. / Kuroki, K. ...Shioi, N. / Tadokoro, T. / Shioi, S. / Hu, Y. / Kurahara, L.H. / Okabe, Y. / Matsubara, H. / Kita, S. / Ose, T. / Kuroki, K. / Maenaka, K. / Terada, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science22121007 Japan
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Crystal structure of the complex between venom toxin and serum inhibitor from Viperidae snake.
Authors: Shioi, N. / Tadokoro, T. / Shioi, S. / Okabe, Y. / Matsubara, H. / Kita, S. / Ose, T. / Kuroki, K. / Terada, S. / Maenaka, K.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine-rich venom protein triflin
B: Small serum protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4386
Polymers36,9672
Non-polymers4724
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-8 kcal/mol
Surface area14470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.166, 48.113, 75.028
Angle α, β, γ (deg.)90.00, 102.61, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Cysteine-rich venom protein triflin / CRVP


Mass: 24826.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Protobothrops flavoviridis (habu) / References: UniProt: Q8JI39
#2: Protein Small serum protein 2 / SSP-2


Mass: 12140.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Protobothrops flavoviridis (habu) / References: UniProt: A7VN14
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: AMMONIUM SULPHATE, MES, PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 17522 / % possible obs: 100 % / Redundancy: 3.8 % / Rsym value: 0.127 / Net I/σ(I): 11.488
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.434 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WVR AND 3IX0

1wvr

3ix0


Resolution: 2.3→39.64 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.69
RfactorNum. reflection% reflection
Rfree0.219 884 5.05 %
Rwork0.186 --
obs0.187 17519 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 30 84 2422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022411
X-RAY DIFFRACTIONf_angle_d0.5153245
X-RAY DIFFRACTIONf_dihedral_angle_d10.445885
X-RAY DIFFRACTIONf_chiral_restr0.021339
X-RAY DIFFRACTIONf_plane_restr0.002420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2956-2.43940.28891430.2262706X-RAY DIFFRACTION99
2.4394-2.62770.27961710.21112752X-RAY DIFFRACTION100
2.6277-2.8920.23451410.2052756X-RAY DIFFRACTION100
2.892-3.31030.23021340.19232774X-RAY DIFFRACTION100
3.3103-4.170.18461330.16752801X-RAY DIFFRACTION100
4.17-39.64620.18991620.16822846X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.85922.46230.86984.81140.54742.3745-0.03620.25470.2007-0.58-0.09060.2683-0.1737-0.170.09810.26520.06250.00760.17-0.01470.172117.465749.20794.6447
25.60231.111-5.73311.0574-1.20866.1871-0.54790.2059-0.9419-0.21540.05120.17541.0261-0.14660.56120.2725-0.01330.01210.1652-0.06730.346714.800534.085812.499
36.45940.7378-3.05542.681-0.1383.7495-0.1264-0.0881-0.22450.1041-0.03030.13410.30880.08720.20270.31220.02220.00060.1561-0.00380.211220.461736.501519.2702
46.55122.1457-2.24222.57740.88293.42210.2607-0.2470.12590.0115-0.33710.5109-0.1136-0.5945-0.06040.1630.0117-0.01930.291-0.04460.29447.470446.720415.5864
51.48940.5196-0.12632.0758-0.20022.37770.0599-0.08730.0391-0.0034-0.12510.0077-0.25830.00570.0570.17090.01130.01430.13210.01150.189621.474451.350813.7586
61.4738-1.4688-0.21456.15340.15398.41810.11290.09990.31260.6036-0.338-1.0180.51280.860.47110.4550.2252-0.1290.75990.02620.766545.576137.974115.8969
71.50770.4754-0.83623.49761.25382.3322-0.00050.25690.72-0.2632-0.2955-2.11850.63171.53530.17640.37180.15920.10640.60910.05630.687142.867443.92068.1678
87.3719-5.06713.14066.6542-2.95086.4161-0.9084-1.11490.75730.84290.0446-0.8382-0.53180.87370.85940.3159-0.0441-0.070.5250.07430.346631.603343.164127.6561
97.47392.33440.86181.3714-1.61535.6821-0.6025-0.31450.72620.95550.30740.04110.73630.13510.30950.55940.06250.00070.2549-0.05710.310329.274438.922942.4392
107.24-4.78274.07487.3609-5.15123.7767-0.1028-0.0396-0.0390.04710.27180.3191-0.0423-0.2458-0.19640.3519-0.0127-0.00140.23160.01260.172823.980939.312534.2397
119.1601-4.62743.71132.7891-1.45464.5111-0.2392-0.4182-0.2543-0.02670.240.2631-0.0428-0.0557-0.03920.2895-0.02290.05120.20470.02130.229715.669745.010825.1594
128.9906-1.21476.57367.7251-1.25324.8727-0.0287-0.6647-0.1872-0.31060.07360.3361-0.1977-0.8652-0.03060.2450.01210.05210.3253-0.03950.20064.755552.85929.9888
133.6973-2.56082.56115.3663-4.63175.4280.1723-0.6061-0.37010.1253-0.01542.2929-1.3557-2.574-0.05220.5720.25810.0560.9891-0.15730.6783-5.327357.193628.5518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 42 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 43 THROUGH 55 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 56 THROUGH 73 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 74 THROUGH 85 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 86 THROUGH 184 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 185 THROUGH 209 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 210 THROUGH 221 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 1 THROUGH 18 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 19 THROUGH 28 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 29 THROUGH 46 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 47 THROUGH 64 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 65 THROUGH 80 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 81 THROUGH 89 )

+
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