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- PDB-6z2p: Crystal structure of catalytic inactive OgpA from Akkermansia muc... -

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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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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