[English] 日本語
Yorodumi
- PDB-7ozc: Sulfated host glycan recognition by carbohydrate sulfatases of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ozc
TitleSulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3109_S1_15)
ComponentsArylsulfatase A
KeywordsHYDROLASE / Host glycans / sulfation / carbohydrate sulfatases / microbiota
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
6-O-sulfo-beta-D-galactopyranose / Arylsulfatase A
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota.
Authors: Luis, A.S. / Basle, A. / Byrne, D.P. / Wright, G.S.A. / London, J.A. / Jin, C. / Karlsson, N.G. / Hansson, G.C. / Eyers, P.A. / Czjzek, M. / Barbeyron, T. / Yates, E.A. / Martens, E.C. / Cartmell, A.
History
DepositionJun 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Arylsulfatase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4423
Polymers57,1411
Non-polymers3002
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-12 kcal/mol
Surface area17530 Å2
Unit cell
Length a, b, c (Å)52.150, 91.760, 52.680
Angle α, β, γ (deg.)90.000, 116.630, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Arylsulfatase A


Mass: 57141.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3109
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A346
#2: 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.: 1 / 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml of BT3109S1_15 with 10 mM 6S-Gal was crystallised in 30 % PEG 4000, 0.2 M ammonium acetate and sodium citrate pH 5.6.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.75→47.136 Å / Num. obs: 44392 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 8.8
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2410 / CC1/2: 0.493

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S20

6s20


Resolution: 1.75→47.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.793 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.217 2071 4.668 %
Rwork0.1836 42295 -
all0.185 --
obs-44366 99.308 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.325 Å2
Baniso -1Baniso -2Baniso -3
1--2.142 Å2-0 Å20.242 Å2
2--0.213 Å2-0 Å2
3---1.122 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 17 186 3934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133999
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173660
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.655454
X-RAY DIFFRACTIONr_angle_other_deg1.3171.5868461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42822.843204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5371522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02925
X-RAY DIFFRACTIONr_nbd_refined0.2030.2775
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23474
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21903
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2205
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.5670.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.27
X-RAY DIFFRACTIONr_nbd_other0.1670.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.21
X-RAY DIFFRACTIONr_mcbond_it1.8542.7722024
X-RAY DIFFRACTIONr_mcbond_other1.8532.7722023
X-RAY DIFFRACTIONr_mcangle_it2.4964.1552558
X-RAY DIFFRACTIONr_mcangle_other2.4964.1552559
X-RAY DIFFRACTIONr_scbond_it2.4153.0181975
X-RAY DIFFRACTIONr_scbond_other2.4173.0191972
X-RAY DIFFRACTIONr_scangle_it3.7034.4252896
X-RAY DIFFRACTIONr_scangle_other3.7044.4262894
X-RAY DIFFRACTIONr_lrange_it4.72132.5044439
X-RAY DIFFRACTIONr_lrange_other4.71132.4454420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.3351310.3363126X-RAY DIFFRACTION98.8767
1.795-1.8450.3021350.3023031X-RAY DIFFRACTION99.3099
1.845-1.8980.3051420.2812964X-RAY DIFFRACTION99.392
1.898-1.9560.2791630.2482857X-RAY DIFFRACTION99.2768
1.956-2.0210.2721280.2352782X-RAY DIFFRACTION99.2835
2.021-2.0910.241040.2132731X-RAY DIFFRACTION99.5785
2.091-2.170.2481320.2032596X-RAY DIFFRACTION99.5257
2.17-2.2590.221550.1782458X-RAY DIFFRACTION99.809
2.259-2.3590.2371370.1752417X-RAY DIFFRACTION99.7656
2.359-2.4740.2171020.1782308X-RAY DIFFRACTION99.6691
2.474-2.6080.2651200.192202X-RAY DIFFRACTION99.871
2.608-2.7660.2151240.1772040X-RAY DIFFRACTION99.6317
2.766-2.9570.2281240.1741908X-RAY DIFFRACTION99.559
2.957-3.1940.189580.1661850X-RAY DIFFRACTION99.4786
3.194-3.4980.176560.1631706X-RAY DIFFRACTION98.9888
3.498-3.910.158680.1451493X-RAY DIFFRACTION98.548
3.91-4.5140.136720.1361312X-RAY DIFFRACTION98.5755
4.514-5.5250.206570.1441127X-RAY DIFFRACTION98.4206
5.525-7.7990.219350.169890X-RAY DIFFRACTION99.1425
7.799-47.090.213280.179497X-RAY DIFFRACTION98.8701

+
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