[English] 日本語
Yorodumi
- PDB-3vt1: Crystal structure of Ct1,3Gal43A in complex with galactose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vt1
TitleCrystal structure of Ct1,3Gal43A in complex with galactose
ComponentsRicin B lectin
KeywordsSUGAR BINDING PROTEIN / GH43 / CBM13 / galactan hydrolysis
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase domain; family 43 ...Ricin-type beta-trefoil lectin domain-like / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Clostridium cellulosome enzymes repeated domain signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Ricin B lectin
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.187 Å
AuthorsJiang, D. / Fan, J. / Wang, X. / Zhao, Y. / Huang, B. / Zhang, X.C.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structure of 1,3Gal43A, an exo-beta-1,3-galactanase from Clostridium thermocellum
Authors: Jiang, D. / Fan, J. / Wang, X. / Zhao, Y. / Huang, B. / Liu, J. / Zhang, X.C.
History
DepositionMay 18, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Ricin B lectin
C: Ricin B lectin
D: Ricin B lectin
E: Ricin B lectin
F: Ricin B lectin
A: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,98113
Polymers351,7206
Non-polymers1,2617
Water00
1
B: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8002
Polymers58,6201
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9803
Polymers58,6201
Non-polymers3602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: Ricin B lectin


Theoretical massNumber of molelcules
Total (without water)58,6201
Polymers58,6201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8002
Polymers58,6201
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9803
Polymers58,6201
Non-polymers3602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
A: Ricin B lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8002
Polymers58,6201
Non-polymers1801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.635, 122.533, 403.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Ricin B lectin


Mass: 58619.980 Da / Num. of mol.: 6 / Fragment: UNP residues 31-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_0661 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DD67
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.18 % / Mosaicity: 0.44 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM sodium acetate, 2.9-3.3M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979305 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979305 Å / Relative weight: 1
ReflectionResolution: 3.187→50 Å / Num. all: 88841 / Num. obs: 88841 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.175 / Χ2: 1.303 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.317.50.55787401.437199.4
3.31-3.457.40.40587671.387199.5
3.45-3.67.40.32987651.389199.6
3.6-3.797.40.26588231.438199.6
3.79-4.037.40.23187761.301199.7
4.03-4.347.40.20488531.367199.7
4.34-4.787.30.17988911.337199.7
4.78-5.477.20.15889201.243199.5
5.47-6.897.10.13390231.133199.8
6.89-506.90.09492830.982198.8

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.187→48.796 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.797 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 1592 1.8 %RANDOM
Rwork0.2355 ---
obs0.2361 88617 99.27 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.719 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 189.52 Å2 / Biso mean: 84.4398 Å2 / Biso min: 37.97 Å2
Baniso -1Baniso -2Baniso -3
1-26.0357 Å20 Å2-0 Å2
2--0.5667 Å2-0 Å2
3----26.6024 Å2
Refinement stepCycle: LAST / Resolution: 3.187→48.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22127 0 84 0 22211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222801
X-RAY DIFFRACTIONf_angle_d0.53230934
X-RAY DIFFRACTIONf_chiral_restr0.0353178
X-RAY DIFFRACTIONf_plane_restr0.0023975
X-RAY DIFFRACTIONf_dihedral_angle_d9.7348135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.187-3.28990.36041410.3167678781998
3.2899-3.40740.30871460.2857811795799
3.4074-3.54380.32031320.27187827795999
3.5438-3.70510.30621480.25577858800699
3.7051-3.90030.29771430.241178588001100
3.9003-4.14460.2491410.224678718012100
4.1446-4.46440.23121490.211178848033100
4.4644-4.91330.20351470.197779608107100
4.9133-5.62330.26361450.222779838128100
5.6233-7.08130.2641440.225980558199100
7.0813-48.80210.28171560.2418240839698

+
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