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- PDB-6z2q: Crystal structure of wild type OgpA from Akkermansia muciniphila ... -

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Basic information

Entry
Database: PDB / ID: 6z2q
TitleCrystal structure of wild type OgpA from Akkermansia muciniphila in complex with an O-glycopeptide (GalGalNAc-TS) product
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 / ACETIC ACID / 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: 2.347 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site
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 ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
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
D: Glycodrosocin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7598
Polymers44,0612
Non-polymers6986
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-64 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.366, 65.366, 187.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AD

#1: Protein O-glycan protease


Mass: 41856.137 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 99 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM sodium HEPES/MOPS pH 7.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate) ...Details: 100mM sodium HEPES/MOPS pH 7.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate) and 50% (w/v) of precipitant mix based on 40% (w/v) PEG 500 MME and 20% (w/v) PEG 20,000 (Morpheus protein crystallization screen).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.347→29.233 Å / Num. obs: 17627 / % possible obs: 98.62 % / Redundancy: 12.7 % / Biso Wilson estimate: 35.98 Å2 / CC1/2: 0.999 / CC star: 0.999 / Rmerge(I) obs: 0.1336 / Rrim(I) all: 0.1391 / Net I/σ(I): 19.29
Reflection shellResolution: 2.347→2.43 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.91 / Num. unique obs: 1530 / CC1/2: 0.2949 / CC star: 0.8 / Rrim(I) all: 1.007 / % possible all: 87.13

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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: 2.347→29.233 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 935 5.31 %
Rwork0.2004 16660 -
obs0.203 17595 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.02 Å2 / Biso mean: 37.1118 Å2 / Biso min: 25.72 Å2
Refinement stepCycle: final / Resolution: 2.347→29.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 66 94 2914
Biso mean--45.04 34.32 -
Num. residues----354
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3473-2.4710.29361140.2531212691
2.471-2.62570.29571430.23812352100
2.6257-2.82830.3211190.24542376100
2.8283-3.11260.30961350.23772389100
3.1126-3.56230.26561430.21282386100
3.5623-4.48550.20951330.16652430100
4.4855-29.2330.21391480.17332601100

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