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- PDB-6z2d: Crystal structure of wild type OgpA from Akkermansia muciniphila ... -

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Basic information

Entry
Database: PDB / ID: 6z2d
TitleCrystal structure of wild type OgpA from Akkermansia muciniphila in P 41 21 2
ComponentsO-glycan protease
KeywordsHYDROLASE / O-glycan endopeptidase / mucins / OgpA. metalloprotease
Function / homologymetal ion binding / FORMIC ACID / Peptidase M43 pregnancy-associated plasma-A domain-containing protein
Function and homology information
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.899 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 15, 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

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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)42,3449
Polymers41,7251
Non-polymers6198
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-55 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.861, 64.861, 187.426
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 , 1 types, 1 molecules A

#1: Protein O-glycan protease


Mass: 41724.938 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

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Non-polymers , 5 types, 161 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium HEPES/MOPS pH 7.5, 100 mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium ...Details: 100 mM sodium HEPES/MOPS pH 7.5, 100 mM carboxylic acids mixture (sodium formate, ammonium acetate, sodium citrate tribasic dihydrate, sodium potassium tartrate tetrahydrate and sodium oxamate), 20% PEG 500 MME and 10% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: DIAMOND / Beamline: I24 / Wavelength: 0.96882 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: 0.96882 Å / Relative weight: 1
ReflectionResolution: 1.899→29.024 Å / Num. obs: 32350 / % possible obs: 99.28 % / Redundancy: 24.9 % / Biso Wilson estimate: 26.11 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0923 / Rrim(I) all: 0.095 / Net I/σ(I): 26.95
Reflection shellResolution: 1.899→1.967 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.84 / Num. unique obs: 2963 / CC1/2: 0.687 / CC star: 0.9 / Rrim(I) all: 0.84

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.899→29.024 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1638 5.06 %
Rwork0.1893 30710 -
obs0.1909 32348 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.9 Å2 / Biso mean: 29.4728 Å2 / Biso min: 13.5 Å2
Refinement stepCycle: final / Resolution: 1.899→29.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 34 153 2944
Biso mean--37.17 32.52 -
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 (%)
1.899-1.95480.3251090.2612230491
1.9548-2.01790.26241320.21782527100
2.0179-2.090.28131380.2142547100
2.09-2.17370.24451320.19722519100
2.1737-2.27260.23891240.1992525100
2.2726-2.39230.22951560.19762539100
2.3923-2.54210.25081470.20372546100
2.5421-2.73830.25511270.19532567100
2.7383-3.01360.22751490.20192562100
3.0136-3.4490.20331380.18922606100
3.449-4.34310.17861360.16982658100
4.3431-29.0240.21031500.1712810100

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