[English] 日本語
Yorodumi
- PDB-9beh: Structure of GH110A in complex with galactose-6-sulfate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9beh
TitleStructure of GH110A in complex with galactose-6-sulfate
ComponentsGH110A
KeywordsSUGAR BINDING PROTEIN / Sulfatase / carrageenan
Function / homology: / 6-O-sulfo-beta-D-galactopyranose
Function and homology information
Biological speciesPseudoalteromonas distincta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.247 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 S1_8C, a lambda-carrageenan specific sulfatase
Authors: Hettle, J.A. / Vickers, C. / Boraston, A.B.
History
DepositionApr 15, 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: GH110A
B: GH110A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,17319
Polymers136,2132
Non-polymers1,96117
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-108 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.112, 77.477, 116.031
Angle α, β, γ (deg.)90.00, 113.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-988-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein GH110A


Mass: 68106.414 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)

-
Sugars , 2 types, 6 molecules

#4: Sugar
ChemComp-G6S / 6-O-sulfo-beta-D-galactopyranose / D-GALACTOSE-6-SULFATE / 6-O-sulfo-beta-D-galactose / 6-O-sulfo-D-galactose / 6-O-sulfo-galactose


Type: D-saccharide, beta linking / Mass: 260.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalp[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
6-sulfo-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-Galp6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Sugar ChemComp-A1APC / 6-O-sulfo-alpha-D-galactopyranose


Type: D-saccharide, alpha linking / Mass: 260.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O9S

-
Non-polymers , 3 types, 606 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25% pentaerythritol propoxylate, 0.05M KCl, 0.05M 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: Aug 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.247→30 Å / Num. obs: 86709 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.065 / Net I/σ(I): 10.6
Reflection shellResolution: 2.247→2.29 Å / Rmerge(I) obs: 0.566 / Num. unique obs: 4700 / CC1/2: 0.815 / Rpim(I) all: 0.373

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.247→19.969 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 4332 5 %
Rwork0.2012 --
obs0.2028 86709 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.247→19.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9135 0 107 595 9837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079435
X-RAY DIFFRACTIONf_angle_d0.90412812
X-RAY DIFFRACTIONf_dihedral_angle_d5.3865600
X-RAY DIFFRACTIONf_chiral_restr0.0611433
X-RAY DIFFRACTIONf_plane_restr0.0061666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2475-2.2730.3389980.25572120X-RAY DIFFRACTION75
2.273-2.29970.28791750.24852585X-RAY DIFFRACTION94
2.2997-2.32770.28711450.24342660X-RAY DIFFRACTION94
2.3277-2.35710.28291340.23622680X-RAY DIFFRACTION96
2.3571-2.38810.28271420.23322670X-RAY DIFFRACTION95
2.3881-2.42070.27691550.24872707X-RAY DIFFRACTION95
2.4207-2.45520.29791370.24952693X-RAY DIFFRACTION96
2.4552-2.49180.28581410.26122717X-RAY DIFFRACTION96
2.4918-2.53070.30321360.24372707X-RAY DIFFRACTION96
2.5307-2.57210.29521430.2442712X-RAY DIFFRACTION97
2.5721-2.61630.27411650.23742672X-RAY DIFFRACTION97
2.6163-2.66380.2881530.23052758X-RAY DIFFRACTION97
2.6638-2.71490.29421490.2462754X-RAY DIFFRACTION98
2.7149-2.77020.27981450.24192786X-RAY DIFFRACTION97
2.7702-2.83030.24841260.24082781X-RAY DIFFRACTION98
2.8303-2.89590.26121610.24742756X-RAY DIFFRACTION99
2.8959-2.96810.28861380.23172830X-RAY DIFFRACTION99
2.9681-3.04810.28551350.23092744X-RAY DIFFRACTION98
3.0481-3.13750.31311570.22822805X-RAY DIFFRACTION99
3.1375-3.23830.25861360.21012821X-RAY DIFFRACTION99
3.2383-3.35350.20641320.20252836X-RAY DIFFRACTION100
3.3535-3.48710.21641540.19592827X-RAY DIFFRACTION100
3.4871-3.64490.20341550.16822821X-RAY DIFFRACTION100
3.6449-3.83580.22511360.17182834X-RAY DIFFRACTION100
3.8358-4.07420.20131410.16972855X-RAY DIFFRACTION100
4.0742-4.38580.17931470.16652820X-RAY DIFFRACTION99
4.3858-4.82150.14711450.15172846X-RAY DIFFRACTION99
4.8215-5.50630.18561530.17142818X-RAY DIFFRACTION99
5.5063-6.88970.2351560.20622838X-RAY DIFFRACTION99
6.8897-19.9690.2181420.20132924X-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