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- PDB-7yx8: Crystal structure of the AM0627 (E326A) inactive mutant in comple... -

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Basic information

Entry
Database: PDB / ID: 7yx8
TitleCrystal structure of the AM0627 (E326A) inactive mutant in complex with PSGL-1-like bis-T glycopeptide and Zn2+
Components
  • PSGL-1-like bis-T glycopeptide
  • Peptidase M60 domain-containing protein
KeywordsHYDROLASE / Glycoprotease / mucinase / T antigen / Tn antigen / AM0627
Function / homology
Function and homology information


M60-like domain, N-terminal / N-terminal domain of M60-like peptidases / Peptidase M60, enhancin-like domain 3 / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Neutral Protease; domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptidase M60 domain-containing protein
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsTaleb, V. / Liao, Q. / Narimatsu, Y. / Garcia-Garcia, A. / Companon, I. / Borges, R.J. / Gonzalez-Ramirez, A.M. / Corzana, F. / Clausen, H. / Rovira, C. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Nat Commun / Year: 2022
Title: Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut.
Authors: Taleb, V. / Liao, Q. / Narimatsu, Y. / Garcia-Garcia, A. / Companon, I. / Borges, R.J. / Gonzalez-Ramirez, A.M. / Corzana, F. / Clausen, H. / Rovira, C. / Hurtado-Guerrero, R.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase M60 domain-containing protein
B: Peptidase M60 domain-containing protein
F: PSGL-1-like bis-T glycopeptide
H: PSGL-1-like bis-T glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,51220
Polymers101,9274
Non-polymers2,58516
Water13,818767
1
A: Peptidase M60 domain-containing protein
H: PSGL-1-like bis-T glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,53213
Polymers50,9642
Non-polymers1,56911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidase M60 domain-containing protein
F: PSGL-1-like bis-T glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9807
Polymers50,9642
Non-polymers1,0165
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.145, 82.687, 172.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: -1 - 505 / Label seq-ID: 4 - 440

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Protein/peptide / Sugars , 3 types, 8 molecules ABFH

#1: Protein Peptidase M60 domain-containing protein


Mass: 49951.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is the construct of the inactive mutant we used for crystallisation purposes. The five glycines in the N-terminus come from the vector. This is why the numbering is different for these glycines in the pdb.
Source: (gene. exp.) Akkermansia muciniphila (bacteria) / Gene: Amuc_0627 / Production host: Escherichia coli (E. coli) / References: UniProt: B2UPI7
#2: Protein/peptide PSGL-1-like bis-T glycopeptide


Mass: 1012.069 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 4 / Source method: obtained synthetically
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 , 3 types, 779 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#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


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Monosaccharides, Buffer system 1 pH 6.5, Precipitant mix 2 (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→172.61 Å / Num. obs: 167774 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 24256 / CC1/2: 0.624

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→86.3 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.668 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18206 6719 4 %RANDOM
Rwork0.167 ---
obs0.16761 160872 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.684 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å2-0 Å20 Å2
2---0.71 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 1.5→86.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 0 273 767 8064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137512
X-RAY DIFFRACTIONr_bond_other_d0.0020.0186996
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.69110152
X-RAY DIFFRACTIONr_angle_other_deg1.481.63816186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05223.008389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.206151243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7851537
X-RAY DIFFRACTIONr_chiral_restr0.0740.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028353
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021727
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.142.253522
X-RAY DIFFRACTIONr_mcbond_other1.1332.2483521
X-RAY DIFFRACTIONr_mcangle_it1.8353.3684394
X-RAY DIFFRACTIONr_mcangle_other1.8363.374395
X-RAY DIFFRACTIONr_scbond_it1.92.6163990
X-RAY DIFFRACTIONr_scbond_other1.8992.6143988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0513.825754
X-RAY DIFFRACTIONr_long_range_B_refined6.30828.4358681
X-RAY DIFFRACTIONr_long_range_B_other6.20127.768504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14926 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 503 -
Rwork0.279 11772 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13250.1013-0.0880.29150.01060.1663-0.0090.0302-0.00690.02380.0046-0.02910.0103-0.00470.00430.0075-0.00620.00150.0161-0.0020.0352-25.8916-8.855930.0174
20.2142-0.1277-0.05070.5642-0.30240.33420.04320.019-0.01870.05780.00240.0132-0.09830.0249-0.04560.0355-00.01730.0355-0.00730.03726.92978.35112.8312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 608
2X-RAY DIFFRACTION2B-1 - 602

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