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- PDB-6z2o: Crystal structure of wild type OgpA from Akkermansia muciniphila ... -

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Basic information

Entry
Database: PDB / ID: 6z2o
TitleCrystal structure of wild type OgpA from Akkermansia muciniphila in P 21 21 21
ComponentsO-glycan protease
KeywordsHYDROLASE / O-glycan endopeptidase / mucins / OgpA. metalloprotease
Function / homologymetal ion binding / Peptidase M43 pregnancy-associated plasma-A domain-containing protein
Function and homology information
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-glycan protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3569
Polymers41,8561
Non-polymers5008
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-17 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.379, 70.170, 94.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100mM sodium imidazole/MES monohydrate pH 6.5, 100mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and ...Details: 100mM sodium imidazole/MES monohydrate pH 6.5, 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 25% (w/v) MPD, 25% (w/v) PEG 1000 and 25% (w/v) PEG 3350 (Morpheus protein crystallization screen).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.1702 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1702 Å / Relative weight: 1
ReflectionResolution: 1.649→29.632 Å / Num. obs: 52999 / % possible obs: 99.66 % / Redundancy: 12.6 % / Biso Wilson estimate: 23.23 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.08763 / Rrim(I) all: 0.09136 / Net I/σ(I): 16.95
Reflection shellResolution: 1.649→1.708 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.5749 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 5089 / CC1/2: 0.1835 / CC star: 0.905 / Rrim(I) all: 0.6045 / % possible all: 97.03

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Processing

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

6z2d


Resolution: 1.649→29.632 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 2729 5.15 %
Rwork0.1904 50267 -
obs0.1915 52996 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.31 Å2 / Biso mean: 27.9432 Å2 / Biso min: 15.42 Å2
Refinement stepCycle: final / Resolution: 1.649→29.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 29 257 3053
Biso mean--34.82 34.75 -
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 (%)
1.649-1.67880.32111210.2374245293
1.6788-1.71110.29451380.21962641100
1.7111-1.7460.23531550.20722569100
1.746-1.7840.22681080.20352663100
1.784-1.82550.22461300.19682634100
1.8255-1.87110.23011350.20072640100
1.8711-1.92170.2191420.20362629100
1.9217-1.97830.22661290.20082643100
1.9783-2.04210.25021380.19792655100
2.0421-2.11510.21171340.20052627100
2.1151-2.19970.2261530.19852635100
2.1997-2.29980.22291430.19442631100
2.2998-2.4210.23981770.20522640100
2.421-2.57260.21871600.2072621100
2.5726-2.77110.20881600.20612638100
2.7711-3.04970.24151240.20142717100
3.0497-3.49040.24241570.19072680100
3.4904-4.39530.16721700.16722710100
4.3953-29.6320.16761550.16762842100

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