[English] 日本語
Yorodumi
- PDB-9s85: Amuc0121_S1_15 in complex with O6 sulfated D-Galactose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s85
TitleAmuc0121_S1_15 in complex with O6 sulfated D-Galactose
ComponentsSulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / mucin / Akkermansia muciniphila / Sulfation
Function / homology
Function and homology information


: / 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 / Sulfatase
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDey, D. / Cartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust225897/Z/22/Z United Kingdom
CitationJournal: To Be Published
Title: The role of Akkermansia muciniphila sulfatases in colonic mucin utilisation
Authors: Dey, D. / Salman, N.D. / Tomlinson, C.W.E. / Gugel, S. / Chunsheng, J. / Reba, G. / Nilsson, M. / McIver, Z. / Simpkin, A. / Davy, M. / Rigden, D.J. / Czjzek, M. / Byrne, D.P. / Case, A. / ...Authors: Dey, D. / Salman, N.D. / Tomlinson, C.W.E. / Gugel, S. / Chunsheng, J. / Reba, G. / Nilsson, M. / McIver, Z. / Simpkin, A. / Davy, M. / Rigden, D.J. / Czjzek, M. / Byrne, D.P. / Case, A. / Baumann, C. / Wright, G.S.A. / van der Post, S. / Martens, E.C. / Yates, E.A. / Davey, L. / Luis, A.S. / Cartmell, A.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfatase
B: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5346
Polymers108,9342
Non-polymers6014
Water5,621312
1
A: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7673
Polymers54,4671
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7673
Polymers54,4671
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.055, 91.127, 160.101
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sulfatase


Mass: 54466.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_0121 / Production host: Escherichia coli (E. coli) / References: UniProt: B2ULS2
#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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus D12- 37. 5 % Precipitant mix 4(25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350), 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE), 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol ...Details: Morpheus D12- 37. 5 % Precipitant mix 4(25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350), 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE), 0.12 M Alcohols (0.2M 1,6-Hexanediol; 0.2M 1-Butanol 0.2M 1,2-Propanediol; 0.2M 2-Propanol; 0.2M 1,4-Butanediol; 0.2M 1,3-Propanediol). 36 mg/ml Amuc0121_C78S, 10 mM O6 sulfated D-galactose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 1, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→60.27 Å / Num. obs: 1210143 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.996 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 61485 / CC1/2: 0.446

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→60.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.906 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2205 4555 5.122 %
Rwork0.185 84377 -
all0.187 --
obs-88932 99.998 %
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: 25.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.095 Å20 Å2-0 Å2
2--0.537 Å2-0 Å2
3----0.632 Å2
Refinement stepCycle: LAST / Resolution: 1.8→60.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7507 0 34 312 7853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0127840
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167483
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.82110611
X-RAY DIFFRACTIONr_angle_other_deg0.5451.78617330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.991550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.275101366
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.25810337
X-RAY DIFFRACTIONr_chiral_restr0.0740.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021732
X-RAY DIFFRACTIONr_nbd_refined0.2090.21510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.26685
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23725
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23990
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2380
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.210
X-RAY DIFFRACTIONr_nbd_other0.1820.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.210
X-RAY DIFFRACTIONr_mcbond_it1.672.3383950
X-RAY DIFFRACTIONr_mcbond_other1.6672.3393950
X-RAY DIFFRACTIONr_mcangle_it2.4324.1944955
X-RAY DIFFRACTIONr_mcangle_other2.4324.1954956
X-RAY DIFFRACTIONr_scbond_it2.7222.6553890
X-RAY DIFFRACTIONr_scbond_other2.7232.6553887
X-RAY DIFFRACTIONr_scangle_it4.3454.715656
X-RAY DIFFRACTIONr_scangle_other4.3454.715657
X-RAY DIFFRACTIONr_lrange_it5.28922.8868616
X-RAY DIFFRACTIONr_lrange_other5.27722.8238569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.333440.3196161X-RAY DIFFRACTION100
1.847-1.8970.2853230.2946028X-RAY DIFFRACTION100
1.897-1.9520.2923120.2785794X-RAY DIFFRACTION100
1.952-2.0120.2843070.2495697X-RAY DIFFRACTION100
2.012-2.0780.2493080.2265520X-RAY DIFFRACTION100
2.078-2.1510.2622720.2185344X-RAY DIFFRACTION100
2.151-2.2320.232840.1985150X-RAY DIFFRACTION100
2.232-2.3230.2312560.1794981X-RAY DIFFRACTION100
2.323-2.4260.2312480.1784779X-RAY DIFFRACTION100
2.426-2.5440.2332580.1814552X-RAY DIFFRACTION100
2.544-2.6820.222390.1714357X-RAY DIFFRACTION100
2.682-2.8440.2432240.1814125X-RAY DIFFRACTION100
2.844-3.040.2122080.1743887X-RAY DIFFRACTION100
3.04-3.2830.1912040.1713626X-RAY DIFFRACTION100
3.283-3.5950.2121560.1713387X-RAY DIFFRACTION100
3.595-4.0180.1721410.153068X-RAY DIFFRACTION100
4.018-4.6360.1581540.1342706X-RAY DIFFRACTION100
4.636-5.6690.1931620.1492280X-RAY DIFFRACTION100
5.669-7.9830.25900.1731845X-RAY DIFFRACTION100
7.983-60.270.178650.1591090X-RAY DIFFRACTION100

+
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