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

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Basic information

Entry
Database: PDB / ID: 6rnn
TitleP46, an immunodominant surface protein from Mycoplasma hyopneumoniae
Components
  • Immunoglobulin heavy chain
  • Immunoglobulin light chain
KeywordsIMMUNE SYSTEM / immunodominant surface protein Mycoplasma hyopneumoniae P46 Monoclonal Antidody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 9, 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 / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / audit_author / cell / citation / citation_author / computing / diffrn_source / pdbx_nonpoly_scheme / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range / 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_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c / _cell.volume / _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 / _pdbx_nonpoly_scheme.auth_seq_num / _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_high / _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_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.pdbx_CC_half / _reflns.pdbx_netI_over_sigmaI / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _struct_mon_prot_cis.pdbx_omega_angle / _symmetry.space_group_name_Hall
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _refine_hist.d_res_high / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Immunoglobulin light chain
D: Immunoglobulin heavy chain
C: Immunoglobulin light chain
H: Immunoglobulin heavy chain


Theoretical massNumber of molelcules
Total (without water)157,0864
Polymers157,0864
Non-polymers00
Water11,656647
1
L: Immunoglobulin light chain
H: Immunoglobulin heavy chain


Theoretical massNumber of molelcules
Total (without water)78,5432
Polymers78,5432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-27 kcal/mol
Surface area19050 Å2
MethodPISA
2
D: Immunoglobulin heavy chain
C: Immunoglobulin light chain


Theoretical massNumber of molelcules
Total (without water)78,5432
Polymers78,5432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-29 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.209, 88.380, 123.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody Immunoglobulin light chain


Mass: 26370.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Immunoglobulin heavy chain


Mass: 52172.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M Sodium Citrate pH 4.0 21% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→61 Å / Num. obs: 94930 / % possible obs: 94.02 % / Redundancy: 18.4 % / CC1/2: 0.98 / Net I/σ(I): 5.92
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 5588 / CC1/2: 0.27

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Processing

Software
NameVersionClassification
PHENIX(dev_2880: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A3R

1a3r


Resolution: 1.95→61 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.261 --
Rwork0.207 --
obs-66671 98.32 %
Displacement parametersBiso mean: 31.1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6463 0 0 647 7110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00686652
X-RAY DIFFRACTIONf_angle_d0.95459107
X-RAY DIFFRACTIONf_chiral_restr0.05781049
X-RAY DIFFRACTIONf_plane_restr0.00631146
X-RAY DIFFRACTIONf_dihedral_angle_d17.90622349

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