[English] 日本語
Yorodumi
- PDB-9s8y: Amuc1074_S1_11 in complex with N-acetyl D-glucosamine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s8y
TitleAmuc1074_S1_11 in complex with N-acetyl D-glucosamine
ComponentsSulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / mucin / Akkermansia muciniphila / Sulfation
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatases signature 1. / Sulfatase, conserved site / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Chem-ETE / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Sulfatase
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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. / Raba, 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. / Raba, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8856
Polymers59,9561
Non-polymers9295
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint9 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.01, 130.01, 86.27
Angle α, β, γ (deg.)90, 90, 90
Int Tables number80
Space group name H-MI41

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Sulfatase


Mass: 59955.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_1074 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UR15

-
Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 440 molecules

#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Morpheus E9: 30 % Precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE) 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M ...Details: Morpheus E9: 30 % Precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000) 0.1 M Buffer system 3 pH 8.5 (Tris (base); BICINE) 0.12 M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol) 20 mg/ml Amuc1074 with 100 mM N-acetyl D-glucosamine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→71.88 Å / Num. obs: 146947 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.998 / Net I/σ(I): 10.7
Reflection shellResolution: 1.38→1.4 Å / Num. unique obs: 7245 / CC1/2: 0.707

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→41.147 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.237 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1841 7209 4.906 %
Rwork0.1673 139720 -
all0.168 --
obs-146929 99.963 %
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: 23.564 Å2
Baniso -1Baniso -2Baniso -3
1--1.328 Å20 Å20 Å2
2---1.328 Å20 Å2
3---2.655 Å2
Refinement stepCycle: LAST / Resolution: 1.38→41.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 46 437 4701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124618
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164260
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.8296274
X-RAY DIFFRACTIONr_angle_other_deg0.6751.7849869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0215567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.745.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70910780
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.28110214
X-RAY DIFFRACTIONr_chiral_restr0.1030.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025533
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021087
X-RAY DIFFRACTIONr_nbd_refined0.2250.2888
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23694
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22202
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2321
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1040.25
X-RAY DIFFRACTIONr_nbd_other0.190.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.211
X-RAY DIFFRACTIONr_mcbond_it1.7412.0992205
X-RAY DIFFRACTIONr_mcbond_other1.7412.0992206
X-RAY DIFFRACTIONr_mcangle_it2.4523.7752793
X-RAY DIFFRACTIONr_mcangle_other2.4523.7752794
X-RAY DIFFRACTIONr_scbond_it3.0732.42413
X-RAY DIFFRACTIONr_scbond_other3.0722.4022414
X-RAY DIFFRACTIONr_scangle_it4.6354.2353481
X-RAY DIFFRACTIONr_scangle_other4.6344.2373482
X-RAY DIFFRACTIONr_lrange_it5.46120.8335268
X-RAY DIFFRACTIONr_lrange_other5.41420.2675173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.38-1.4160.3245370.327102610.327107990.8620.8699.99070.326
1.416-1.4550.3054810.308100720.307105530.8810.8791000.301
1.455-1.4970.265050.26997620.268102670.910.911000.257
1.497-1.5430.2414650.23795440.237100100.9330.93599.990.22
1.543-1.5930.2265170.21791280.21896450.9480.9531000.199
1.593-1.6490.2074350.18589000.18693350.9640.971000.168
1.649-1.7110.1834630.16385980.16490610.9740.9791000.149
1.711-1.7810.1884210.15382760.15586970.9730.9831000.142
1.781-1.860.1814110.15379170.15583300.9780.98599.9760.145
1.86-1.9510.1793640.14875920.1579560.980.9861000.144
1.951-2.0560.1813800.15972170.1675990.980.98599.97370.157
2.056-2.180.1754040.15767570.15871740.9810.98699.81880.161
2.18-2.330.1813660.15563930.15667770.9790.98699.73440.163
2.33-2.5160.1763120.14759600.14862720.980.9871000.16
2.516-2.7550.1693090.14255100.14458190.9820.9871000.163
2.755-3.0790.1862540.16450130.16552690.9790.98399.9620.191
3.079-3.5520.1961980.17444410.17546400.980.98399.97840.202
3.552-4.3420.151570.14437830.14539470.9890.98899.82270.183
4.342-6.1070.151340.15229210.15230590.9920.99199.86920.202
6.107-41.1470.162960.17516730.17417690.9830.9871000.226

+
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