[English] 日本語
Yorodumi
- PDB-7ana: A single sulfatase is required for metabolism of colonic mucin O-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ana
TitleA single sulfatase is required for metabolism of colonic mucin O-glycans and intestinal colonization by a symbiotic human gut bacterium (BT1622-S1_20)
ComponentsN-acetylgalactosamine-6-sulfatase
KeywordsHYDROLASE / Carbohydrate sulfatase / mucin / microbiome / bacteroides
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetylgalactosamine-6-sulfatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSofia de Jesus Vaz Luis, A. / Basle, A. / Martens, E.C. / Cartmell, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustSBF0051065163470 United Kingdom
CitationJournal: Nature / Year: 2021
Title: A single sulfatase is required to access colonic mucin by a gut bacterium.
Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, ...Authors: Luis, A.S. / Jin, C. / Pereira, G.V. / Glowacki, R.W.P. / Gugel, S.R. / Singh, S. / Byrne, D.P. / Pudlo, N.A. / London, J.A. / Basle, A. / Reihill, M. / Oscarson, S. / Eyers, P.A. / Czjzek, M. / Michel, G. / Barbeyron, T. / Yates, E.A. / Hansson, G.C. / Karlsson, N.G. / Cartmell, A. / Martens, E.C.
History
DepositionOct 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / refine / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _refine.pdbx_diffrn_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: N-acetylgalactosamine-6-sulfatase
BBB: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4588
Polymers113,6522
Non-polymers8066
Water3,009167
1
AAA: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0873
Polymers56,8261
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-acetylgalactosamine-6-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3705
Polymers56,8261
Non-polymers5454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.246, 83.246, 390.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 26 - 500 / Label seq-ID: 29 - 503

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AAABBB

#1: Protein N-acetylgalactosamine-6-sulfatase


Mass: 56825.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1622 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A7A3

-
Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 170 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20 % PEG 3350, 0.2 M sodium citrate 30 mg/ml BT1622 with 100 mM GalNAc.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→70.221 Å / Num. obs: 62514 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.999 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 4532 / CC1/2: 0.84

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BT1624

Resolution: 2.3→70.221 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.208 / SU B: 14.473 / SU ML: 0.167 / Average fsc free: 0.9133 / Average fsc work: 0.9177 / Cross valid method: FREE R-VALUE / ESU R: 0.26 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2347 3080 4.932 %
Rwork0.2111 59372 -
all0.212 --
obs-62452 99.898 %
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: 58.047 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å2-0 Å2
2--1.07 Å20 Å2
3----2.141 Å2
Refinement stepCycle: LAST / Resolution: 2.3→70.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7570 0 51 167 7788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157086
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.66210664
X-RAY DIFFRACTIONr_angle_other_deg1.1621.58816389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64722.676426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.117151247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8281541
X-RAY DIFFRACTIONr_chiral_restr0.060.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021875
X-RAY DIFFRACTIONr_nbd_refined0.1880.21398
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.26577
X-RAY DIFFRACTIONr_nbtor_refined0.1610.23740
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2244
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.210
X-RAY DIFFRACTIONr_nbd_other0.2440.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1340.23
X-RAY DIFFRACTIONr_mcbond_it0.9053.1463803
X-RAY DIFFRACTIONr_mcbond_other0.9053.1453802
X-RAY DIFFRACTIONr_mcangle_it1.4924.7174752
X-RAY DIFFRACTIONr_mcangle_other1.4924.7174753
X-RAY DIFFRACTIONr_scbond_it1.0043.2394055
X-RAY DIFFRACTIONr_scbond_other1.0043.2394056
X-RAY DIFFRACTIONr_scangle_it1.6734.815912
X-RAY DIFFRACTIONr_scangle_other1.6734.815913
X-RAY DIFFRACTIONr_lrange_it3.51335.8358537
X-RAY DIFFRACTIONr_lrange_other3.50935.7898527
X-RAY DIFFRACTIONr_ncsr_local_group_10.050.0516368
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.050410.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.050410.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3062130.2894314X-RAY DIFFRACTION99.9338
2.36-2.4240.2752150.284167X-RAY DIFFRACTION99.8405
2.424-2.4950.3012170.2794089X-RAY DIFFRACTION99.9072
2.495-2.5710.2971970.2593993X-RAY DIFFRACTION99.857
2.571-2.6560.2562030.2423842X-RAY DIFFRACTION99.9506
2.656-2.7490.2531930.233743X-RAY DIFFRACTION99.9238
2.749-2.8530.2511940.2243613X-RAY DIFFRACTION99.8165
2.853-2.9690.2711870.2263479X-RAY DIFFRACTION99.891
2.969-3.1010.2581920.2333354X-RAY DIFFRACTION99.9155
3.101-3.2530.2461780.2393161X-RAY DIFFRACTION99.9401
3.253-3.4290.2521590.233060X-RAY DIFFRACTION99.9379
3.429-3.6370.2361370.2272934X-RAY DIFFRACTION99.9349
3.637-3.8880.2441300.2072743X-RAY DIFFRACTION99.8957
3.888-4.1990.2091400.182590X-RAY DIFFRACTION100
4.199-4.60.2181220.1622374X-RAY DIFFRACTION99.9199
4.6-5.1430.1841220.1592160X-RAY DIFFRACTION99.9124
5.143-5.9380.216910.1821955X-RAY DIFFRACTION99.9511
5.938-7.2720.202770.1981657X-RAY DIFFRACTION100
7.272-10.2830.165700.1771343X-RAY DIFFRACTION99.9293
10.283-70.2210.29430.271801X-RAY DIFFRACTION98.829
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.10070.57042.01181.00550.62863.14170.08960.5094-0.2392-0.25790.1511-0.24820.1610.8056-0.24070.3190.0777-0.0060.5063-0.04850.08247.4878-33.12660.2635
21.2728-0.1002-0.24911.8379-0.04381.7609-0.0502-0.0555-0.0321-0.03050.09250.1084-0.1621-0.0747-0.04240.25980.0234-0.04850.0190.00580.0195-25.4473-35.9183-40.2112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA26 - 500
2X-RAY DIFFRACTION1ALLAaA601
3X-RAY DIFFRACTION2ALLBBB26 - 500
4X-RAY DIFFRACTION2ALLBaB601

+
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