[English] 日本語
Yorodumi
- PDB-6z2p: Crystal structure of catalytic inactive OgpA from Akkermansia muc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z2p
TitleCrystal structure of catalytic inactive OgpA from Akkermansia muciniphila in complex with an O-glycopeptide (glycodrosocin) substrate
Components
  • Glycodrosocin
  • O-glycan protease
KeywordsHYDROLASE / O-glycan endopeptidase / mucins / OgpA. metalloprotease
Function / homology
Function and homology information


positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / defense response to insect / response to bacterium / defense response / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / extracellular region / metal ion binding
Similarity search - Function
Thomsen-Friedenreich antigen / Peptidase M43 pregnancy-associated plasma-A domain-containing protein / Drosocin antimicrobial peptides
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsTrastoy, B. / Naegali, A. / Anso, I. / Sjogren, J. / Guerin, M.E.
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila.
Authors: Trastoy, B. / Naegeli, A. / Anso, I. / Sjogren, J. / Guerin, M.E.
History
DepositionMay 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.title ..._citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 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
A: O-glycan protease
C: Glycodrosocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3594
Polymers43,9362
Non-polymers4232
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-4 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.920, 126.920, 65.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein O-glycan protease


Mass: 41731.031 Da / Num. of mol.: 1 / Mutation: H205A, D206A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_1119 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UR60
#2: Protein/peptide Glycodrosocin


Mass: 2204.579 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P36193*PLUS
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM MIB pH 5.0 and 25% (w/v) PEG 1,500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979181 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979181 Å / Relative weight: 1
ReflectionResolution: 2.16→44.873 Å / Num. obs: 27920 / % possible obs: 99.02 % / Redundancy: 2 % / Biso Wilson estimate: 51.51 Å2 / CC1/2: 0.992 / CC star: 0.999 / Rmerge(I) obs: 0.02598 / Rrim(I) all: 0.03675 / Net I/σ(I): 14.42
Reflection shellResolution: 2.16→2.238 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 2619 / CC1/2: 0.433 / CC star: 0.695 / Rrim(I) all: 0.6123 / % possible all: 93.63

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z2D

6z2d


Resolution: 2.16→44.873 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.12 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 2676 5.04 %
Rwork0.1988 50441 -
obs0.2005 27837 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.49 Å2 / Biso mean: 54.1285 Å2 / Biso min: 31.06 Å2
Refinement stepCycle: final / Resolution: 2.16→44.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 26 38 2897
Biso mean--53.55 49.77 -
Num. residues----365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1605-2.19980.32331200.3096222481
2.1998-2.24210.37191440.317263497
2.2421-2.28780.35991400.3464263197
2.2878-2.33760.34011470.3444274397
2.3376-2.3920.32041410.2989266498
2.392-2.45180.38961370.2958264297
2.4518-2.51810.3171440.2794268097
2.5181-2.59210.30191420.2545267098
2.5921-2.67580.27361400.2322266498
2.6758-2.77140.29881430.2383265497
2.7714-2.88240.26891430.2357268998
2.8824-3.01350.32621420.2331268498
3.0135-3.17240.25361470.2235271799
3.1724-3.37110.29521380.219266099
3.3711-3.63120.22261390.2074268897
3.6312-3.99650.19521390.1654270698
3.9965-4.57430.14721430.1405270399
4.5743-5.76120.16011410.1525267498
5.7612-44.8730.21071460.1603271498

+
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://pdbjlvh1.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