[English] 日本語
Yorodumi
- PDB-5gwf: FraC with GlcNAc(6S) bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gwf
TitleFraC with GlcNAc(6S) bound
ComponentsDELTA-actitoxin-Afr1a
KeywordsTOXIN / ACTINOPORIN / PORE-FORMING TOXIN / CARBOHYDRATE-PROTEIN INTERACTION / LIPID-PROTEIN INTERACTION / CYTOLYSIN / NANOPORE
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / channel activity / pore complex / monoatomic cation transport / toxin activity / lipid binding / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / Sea anemone cytotoxic protein / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-NGY / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCaaveiro, J.M.M. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS25249115 Japan
JSPS15K06962 Japan
CitationJournal: Philos. Trans. R. Soc. Lond., B, Biol. Sci. / Year: 2017
Title: Haemolytic actinoporins interact with carbohydrates using their lipid-binding module
Authors: Tanaka, K. / Caaveiro, J.M.M. / Morante, K. / Tsumoto, K.
History
DepositionSep 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DELTA-actitoxin-Afr1a
B: DELTA-actitoxin-Afr1a
C: DELTA-actitoxin-Afr1a
D: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,75821
Polymers79,5104
Non-polymers1,24817
Water13,727762
1
A: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9132
Polymers19,8771
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8070 Å2
MethodPISA
2
B: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4849
Polymers19,8771
Non-polymers6068
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area8090 Å2
MethodPISA
3
C: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0765
Polymers19,8771
Non-polymers1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area8020 Å2
MethodPISA
4
D: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2855
Polymers19,8771
Non-polymers4084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 44.400, 114.360
Angle α, β, γ (deg.)90.00, 92.76, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
DELTA-actitoxin-Afr1a / DELTA-AITX-Afr1a / Cytolysin fragaceatoxin C / fraC


Mass: 19877.498 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia fragacea (sea anemone) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B9W5G6
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-NGY / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-alpha-D-glucopyranose / N-acetyl-6-O-sulfo-alpha-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, alpha linking / Mass: 301.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO9S
IdentifierTypeProgram
DGlcpNAc[6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 18% PEG8000, 210mM ammonium sulfate, 100mM sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→37.06 Å / Num. obs: 103405 / % possible obs: 91.8 % / Redundancy: 5.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.8
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.5 / CC1/2: 0.937 / % possible all: 76.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWI

3vwi


Resolution: 1.55→37.06 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.307 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16307 3161 3.1 %RANDOM
Rwork0.11761 ---
obs0.11895 100243 91.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.55→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 63 762 6361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195909
X-RAY DIFFRACTIONr_bond_other_d0.0020.025541
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9348061
X-RAY DIFFRACTIONr_angle_other_deg0.995312712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49822.889270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08715947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4171542
X-RAY DIFFRACTIONr_chiral_restr0.1010.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026875
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021505
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_it1.4621.3222908
X-RAY DIFFRACTIONr_mcbond_other1.461.3192903
X-RAY DIFFRACTIONr_mcangle_it1.6561.9813645
X-RAY DIFFRACTIONr_mcangle_other1.6571.9813644
X-RAY DIFFRACTIONr_scbond_it2.341.6333001
X-RAY DIFFRACTIONr_scbond_other2.3391.6333001
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6272.3414384
X-RAY DIFFRACTIONr_long_range_B_refined3.05212.5767247
X-RAY DIFFRACTIONr_long_range_B_other2.6411.8246853
X-RAY DIFFRACTIONr_rigid_bond_restr3.953311450
X-RAY DIFFRACTIONr_sphericity_free18.2275259
X-RAY DIFFRACTIONr_sphericity_bonded5.979511808
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 189 -
Rwork0.134 5617 -
obs--69.6 %

+
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://pdbjlvh1.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