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

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Basic information

Entry
Database: PDB / ID: 6rux
TitleP46, an immunodominant surface protein from Mycoplasma hyopneumoniae
Components46 kDa surface antigen
KeywordsPROTEIN BINDING / immunodominant surface protein Mycoplasma hyopneumoniae P46
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.
Similarity search - Domain/homology
alpha-maltose / 46 kDa surface antigen
Similarity search - Component
Biological speciesMycoplasma hyopneumoniae J (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionMay 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 2.0Jun 17, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / audit_author / cell / chem_comp / citation / citation_author / computing / diffrn_source / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / reflns_shell / struct_conf / struct_conn / struct_ncs_dom / struct_ncs_dom_lim / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen / symmetry
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.occupancy / _atom_site.type_symbol / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _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 / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _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.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_diffrn_id / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _symmetry.space_group_name_Hall
Description: Ligand identity / Provider: author / Type: Coordinate replacement
Revision 3.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 24, 2024Group: Data collection / Database references ...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
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: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3759
Polymers127,2803
Non-polymers1,0966
Water1,71195
1
A: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7923
Polymers42,4271
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7923
Polymers42,4271
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7923
Polymers42,4271
Non-polymers3652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.178, 136.178, 139.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein 46 kDa surface antigen / p46


Mass: 42426.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma hyopneumoniae J (bacteria) / Strain: J / ATCC 25934 / NCTC 10110 / Gene: p46, MHJ_0511
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0C0J8
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5 0.2 M Sodium Acetate 32% PEG 4000 3% Maltose

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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 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: 2.5→60 Å / Num. obs: 52027 / % possible obs: 60 % / Redundancy: 9.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.02993 / Net I/σ(I): 35.42
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 5152 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RQG

6rqg


Resolution: 2.5→60 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.268 --RANDOM
Rwork0.209 ---
obs-52027 99.94 %-
Displacement parametersBiso mean: 75.8 Å2
Refinement stepCycle: LAST / Resolution: 2.5→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8604 0 72 95 8771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00878826
X-RAY DIFFRACTIONf_angle_d1.014511952
X-RAY DIFFRACTIONf_chiral_restr0.05651357
X-RAY DIFFRACTIONf_plane_restr0.00721550
X-RAY DIFFRACTIONf_dihedral_angle_d20.6753310

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