[English] 日本語
Yorodumi
- PDB-9beu: Structure of GH110B in complex with a lambda-carrageenan oligosac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9beu
TitleStructure of GH110B in complex with a lambda-carrageenan oligosaccharide
ComponentsGlycoside hydrolase family 110
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Function / homology
Function and homology information


: / GLAA-B beta-barrel domain II / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
IODIDE ION / Glycoside hydrolase family 110
Similarity search - Component
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHettle, J.A. / Vickers, C. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: To Be Published
Title: Structure of GH110B in complex with a lambda-carrageenan oligosaccharide
Authors: Hettle, J.A. / Vickers, C. / Boraston, A.B.
History
DepositionApr 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside hydrolase family 110
B: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,60179
Polymers139,6912
Non-polymers8,91077
Water3,783210
1
A: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,17139
Polymers69,8461
Non-polymers4,32638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside hydrolase family 110
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,43040
Polymers69,8461
Non-polymers4,58539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.463, 128.350, 98.905
Angle α, β, γ (deg.)90.00, 122.15, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glycoside hydrolase family 110 / GH110B


Mass: 69845.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas distincta (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8I3AZV9
#2: Polysaccharide alpha-D-galactopyranose-(1-3)-2-O-sulfo-beta-D-galactopyranose-(1-4)-2,6-di-O-sulfo-alpha-D- ...alpha-D-galactopyranose-(1-3)-2-O-sulfo-beta-D-galactopyranose-(1-4)-2,6-di-O-sulfo-alpha-D-galactopyranose-(1-3)-2-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 986.830 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
[][b-D-Galp2SO3]{[(3+1)][a-D-Galp2SO36SO3]{[(4+1)][b-D-Galp2SO3]{[(3+1)][a-D-Galp]{}}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 285 molecules

#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: I
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 18 % PEG 3350, 0.725 M NaI, 2% Tacsimate, 2.5% glycerol, 0.1 M HEPES (pH 7.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 69196 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.059 / Net I/σ(I): 11.5
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.479 / Num. unique obs: 3433 / CC1/2: 0.803 / Rpim(I) all: 0.332

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.963 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 3496 5.09 %
Rwork0.1969 --
obs0.1993 68675 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 230 210 9580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089491
X-RAY DIFFRACTIONf_angle_d0.99112849
X-RAY DIFFRACTIONf_dihedral_angle_d5.4156635
X-RAY DIFFRACTIONf_chiral_restr0.0621454
X-RAY DIFFRACTIONf_plane_restr0.0051650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4004-2.43320.26771250.23642382X-RAY DIFFRACTION91
2.4332-2.4680.29731190.24342574X-RAY DIFFRACTION97
2.468-2.50480.28511370.23722555X-RAY DIFFRACTION97
2.5048-2.54390.2891400.24012558X-RAY DIFFRACTION98
2.5439-2.58560.29031330.24482641X-RAY DIFFRACTION99
2.5856-2.63020.29291350.24592589X-RAY DIFFRACTION99
2.6302-2.6780.30521410.23422605X-RAY DIFFRACTION100
2.678-2.72940.33791510.23882610X-RAY DIFFRACTION100
2.7294-2.78510.30931330.2532649X-RAY DIFFRACTION100
2.7851-2.84560.34491710.26322576X-RAY DIFFRACTION100
2.8456-2.91180.32871530.26742628X-RAY DIFFRACTION99
2.9118-2.98450.38051710.25842565X-RAY DIFFRACTION99
2.9845-3.06510.30631480.23612615X-RAY DIFFRACTION100
3.0651-3.15520.30741480.23952577X-RAY DIFFRACTION99
3.1552-3.2570.25031200.21442653X-RAY DIFFRACTION99
3.257-3.37320.27461460.20892623X-RAY DIFFRACTION100
3.3732-3.50810.20461250.18682635X-RAY DIFFRACTION100
3.5081-3.66750.21341330.17072676X-RAY DIFFRACTION99
3.6675-3.86050.20751520.16452585X-RAY DIFFRACTION100
3.8605-4.10180.18691430.16862611X-RAY DIFFRACTION99
4.1018-4.41750.17591300.15272647X-RAY DIFFRACTION99
4.4175-4.86040.16391070.13912620X-RAY DIFFRACTION99
4.8604-5.55980.21851480.16782655X-RAY DIFFRACTION99
5.5598-6.99010.23851480.20172649X-RAY DIFFRACTION100
6.9901-29.9630.22181390.19742701X-RAY DIFFRACTION99

+
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