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- PDB-6s3t: P46, an immunodominant surface protein from Mycoplasma hyopneumoniae -

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Basic information

Entry
Database: PDB / ID: 6s3t
TitleP46, an immunodominant surface protein from Mycoplasma hyopneumoniae
Components
  • 46 kDa surface antigen
  • Immunoglobulin heavy chain
  • Immunoglobulin light chain
KeywordsPROTEIN BINDING / immunodominant surface protein Mycoplasma hyopneumoniae P46 Complex with monolonal antibody
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / carbohydrate binding / plasma membrane
Similarity search - Function
: / : / Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-xylopyranose / 46 kDa surface antigen
Similarity search - Component
Biological speciesMycoplasma hyopneumoniae J (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGuasch, A. / Gonzalez-Gonzalez, L. / Fita, I.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2015-71092-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure of P46, an immunodominant surface protein from Mycoplasma hyopneumoniae: interaction with a monoclonal antibody.
Authors: Guasch, A. / Montane, J. / Moros, A. / Pinol, J. / Sitja, M. / Gonzalez-Gonzalez, L. / Fita, I.
History
DepositionJun 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 2.0May 27, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / audit_author / chem_comp / citation / citation_author / diffrn_source / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_peptide_omega.auth_asym_id_1 / _pdbx_validate_peptide_omega.auth_asym_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.d_res_low / _reflns.number_obs / _reflns.percent_possible_obs / _reflns_shell.d_res_low / _reflns_shell.number_unique_obs / _struct_mon_prot_cis.pdbx_omega_angle
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_close_contact / refine_hist
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_atom_id_2 / _refine_hist.d_res_low
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 46 kDa surface antigen
B: 46 kDa surface antigen
C: Immunoglobulin light chain
D: Immunoglobulin heavy chain
I: Immunoglobulin light chain
E: Immunoglobulin heavy chain
M: Immunoglobulin light chain
N: Immunoglobulin heavy chain
Q: Immunoglobulin light chain
R: Immunoglobulin heavy chain
S: 46 kDa surface antigen
T: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)484,57120
Polymers483,87912
Non-polymers6928
Water00
1
A: 46 kDa surface antigen
M: Immunoglobulin light chain
N: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1435
Polymers120,9703
Non-polymers1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 46 kDa surface antigen
Q: Immunoglobulin light chain
R: Immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1435
Polymers120,9703
Non-polymers1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunoglobulin light chain
D: Immunoglobulin heavy chain
S: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1435
Polymers120,9703
Non-polymers1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Immunoglobulin light chain
E: Immunoglobulin heavy chain
T: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,1435
Polymers120,9703
Non-polymers1732
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)261.981, 185.010, 197.122
Angle α, β, γ (deg.)90.000, 134.430, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein
46 kDa surface antigen / p46


Mass: 42426.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma hyopneumoniae J (bacteria) / Gene: p46, MHJ_0511
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0C0J8
#2: Antibody
Immunoglobulin light chain


Mass: 26370.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody
Immunoglobulin heavy chain


Mass: 52172.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M MIB pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→29.3 Å / Num. obs: 83357 / % possible obs: 98.8 % / Redundancy: 1.9 % / CC1/2: 0.981 / Net I/σ(I): 5.51
Reflection shellResolution: 3.5→3.6 Å / Num. unique obs: 8278 / CC1/2: 0.292

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RQG, 6RNN

6rqg

6rnn


Resolution: 3.5→29 Å / Cross valid method: FREE R-VALUE / σ(F): 2.4 / Phase error: 31.8932
RfactorNum. reflection% reflection
Rfree0.273 4283 5.34 %
Rwork0.247 --
obs0.2424 83325 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 103.39 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24934 0 44 0 24978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325532
X-RAY DIFFRACTIONf_angle_d0.630634769
X-RAY DIFFRACTIONf_chiral_restr0.04233959
X-RAY DIFFRACTIONf_plane_restr0.00444460
X-RAY DIFFRACTIONf_dihedral_angle_d15.84389239
LS refinement shellResolution: 3.5→29.3 Å
RfactorNum. reflection% reflection
Rfree0.1981 248 -
Rwork0.1787 3972 -
obs--92.59 %

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