[English] 日本語
Yorodumi
- PDB-3bx4: Crystal structure of the snake venom toxin aggretin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bx4
TitleCrystal structure of the snake venom toxin aggretin
Components
  • Aggretin alpha chain
  • Aggretin beta chain
KeywordsTOXIN
Function / homology
Function and homology information


regulation of cytokine activity / toxin activity / extracellular region / metal ion binding
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Snaclec rhodocytin subunit beta / Snaclec rhodocytin subunit alpha
Similarity search - Component
Biological speciesAgkistrodon rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHooley, E. / Papagrigoriou, E. / Navdaev, A. / Pandey, A. / Clemetson, J.M. / Clemetson, K.J. / Emsley, J.
CitationJournal: Biochemistry / Year: 2008
Title: The crystal structure of the platelet activator aggretin reveals a novel (alphabeta)2 dimeric structure.
Authors: Hooley, E. / Papagrigoriou, E. / Navdaev, A. / Pandey, A.V. / Clemetson, J.M. / Clemetson, K.J. / Emsley, J.
History
DepositionJan 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aggretin alpha chain
B: Aggretin beta chain
C: Aggretin alpha chain
D: Aggretin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,16214
Polymers65,2054
Non-polymers95710
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.318, 91.305, 118.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU5AA6 - 1346 - 134
21ASPASPLEULEU5CC6 - 1346 - 134
12SERSERPHEPHE4BB4 - 12127 - 144
22SERSERPHEPHE4DD4 - 12127 - 144

NCS ensembles :
ID
1
2

-
Components

#1: Protein Aggretin alpha chain


Mass: 15812.376 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Agkistrodon rhodostoma (Malayan pit viper)
Secretion: venom / References: UniProt: Q9I841
#2: Protein Aggretin beta chain


Mass: 16790.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Agkistrodon rhodostoma (Malayan pit viper)
Secretion: venom / References: UniProt: Q9I840
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.4M ammonium sulphate, 25mM ammonium acetate, 2% isopropanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2003 / Details: mirrors
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→14.91 Å / Num. obs: 77418 / % possible obs: 100 % / Observed criterion σ(I): 2.6
Reflection shellResolution: 1.7→1.744 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVU

1fvu


Resolution: 1.7→14.91 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.121 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 3853 5 %RANDOM
Rwork0.20236 ---
all0.20404 73565 --
obs0.20404 73565 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.968 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 51 324 4564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214320
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9085873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64324.844225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6815675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5821513
X-RAY DIFFRACTIONr_chiral_restr0.1350.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023363
X-RAY DIFFRACTIONr_nbd_refined0.2140.21932
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.218
X-RAY DIFFRACTIONr_mcbond_it1.3371.52587
X-RAY DIFFRACTIONr_mcangle_it2.17324052
X-RAY DIFFRACTIONr_scbond_it2.92932056
X-RAY DIFFRACTIONr_scangle_it4.2514.51818
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A513medium positional0.240.5
2B947medium positional0.440.5
1A516loose positional0.645
1A513medium thermal2.592
2B947medium thermal2.872
1A516loose thermal3.0510
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 270 -
Rwork0.273 5312 -
obs--100 %

+
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