[English] 日本語
Yorodumi
- PDB-6rqg: P46, an immunodominant surface protein from Mycoplasma hyopneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rqg
TitleP46, an immunodominant surface protein from Mycoplasma hyopneumoniae
Components46 kDa surface antigen
KeywordsPROTEIN BINDING / immunodominant surface protein Mycoplasma hyopneumoniae P46
Function / homologyPeriplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / 46 kDa surface antigen
Function and homology information
Biological speciesMycoplasma hyopneumoniae J (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGuasch, A. / 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 Crys Section D / Year: 2020
Title: Structure of P46, an immunodominant surface 58 protein from Mycoplasma hyopneumoniae:interaction with a monoclonal antibody
Authors: Guasch, A. / Montane, J. / Moros, A. / Pinyol, J. / Sitja, M. / Gonzalez-Gonzalez, L. / Fita, I.
History
DepositionMay 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Other / Category: cell
Item: _cell.Z_PDB / _cell.length_a ..._cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.2Jan 29, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 2.0Jun 3, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / cell / chem_comp / citation / citation_author / computing / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct_asym / struct_conf / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site / struct_site_gen / symmetry
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _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 / _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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_strain / _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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_num_residues / _symmetry.space_group_name_Hall
Description: Ligand identity / 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 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)127,3486
Polymers127,2803
Non-polymers693
Water362
1
A: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4492
Polymers42,4271
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4492
Polymers42,4271
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 46 kDa surface antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4492
Polymers42,4271
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.478, 136.478, 139.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVAL(chain 'A' and (resid 43 through 124 or resid 129...AA43 - 12212 - 91
12THRTHRTHRTHR(chain 'A' and (resid 43 through 124 or resid 129...AA12493
13ILEILEASNASN(chain 'A' and (resid 43 through 124 or resid 129...AA129 - 23098 - 199
14GLNGLNASNASN(chain 'A' and (resid 43 through 124 or resid 129...AA232 - 362201 - 331
15ARGARGASNASN(chain 'A' and (resid 43 through 124 or resid 129...AA366 - 386335 - 355
16THRTHRVALVAL(chain 'A' and (resid 43 through 124 or resid 129...AA388 - 391357 - 360
17ASNASNVALVAL(chain 'A' and (resid 43 through 124 or resid 129...AA395 - 401364 - 370
18PROPROASPASP(chain 'A' and (resid 43 through 124 or resid 129...AA403 - 415372 - 384
29ALAALAVALVAL(chain 'B' and (resid 43 through 124 or resid 129...BB43 - 12212 - 91
210THRTHRTHRTHR(chain 'B' and (resid 43 through 124 or resid 129...BB12493
211ILEILEASNASN(chain 'B' and (resid 43 through 124 or resid 129...BB129 - 23098 - 199
212GLNGLNASNASN(chain 'B' and (resid 43 through 124 or resid 129...BB232 - 362201 - 331
213ARGARGASNASN(chain 'B' and (resid 43 through 124 or resid 129...BB366 - 386335 - 355
214THRTHRVALVAL(chain 'B' and (resid 43 through 124 or resid 129...BB388 - 391357 - 360
215ASNASNVALVAL(chain 'B' and (resid 43 through 124 or resid 129...BB395 - 401364 - 370
216PROPROASPASP(chain 'B' and (resid 43 through 124 or resid 129...BB403 - 415372 - 384
317ALAALAVALVAL(chain 'C' and (resid 43 through 230 or resid 232...CC43 - 12212 - 91
318THRTHRASNASN(chain 'C' and (resid 43 through 230 or resid 232...CC128 - 23097 - 199
319GLNGLNASNASN(chain 'C' and (resid 43 through 230 or resid 232...CC232 - 362201 - 331
320ARGARGASNASN(chain 'C' and (resid 43 through 230 or resid 232...CC366 - 386335 - 355
321THRTHRVALVAL(chain 'C' and (resid 43 through 230 or resid 232...CC388 - 391357 - 360
322ASNASNVALVAL(chain 'C' and (resid 43 through 230 or resid 232...CC395 - 401364 - 370
323PROPROASPASP(chain 'C' and (resid 43 through 230 or resid 232...CC403 - 415372 - 384

-
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) / Gene: p46, MHJ_0511
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0C0J8
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5 0.2 M Sodium Acetate 32% PEG 4000

-
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: 3.1→58.9 Å / Num. obs: 26816 / % possible obs: 97.59 % / Redundancy: 10.56 % / Biso Wilson estimate: 85.99 Å2 / CC1/2: 0.97 / Net I/σ(I): 22.88
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 1.9 % / Num. unique obs: 4774 / CC1/2: 0.17

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YWH, 3URM, 4WWH

4ywh

3urm

4wwh


Resolution: 3.1→54.39 Å / SU ML: 0.4118 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 1380 5.16 %
Rwork0.2033 25359 -
obs0.2057 26739 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.85 Å2
Refinement stepCycle: LAST / Resolution: 3.1→54.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8580 0 3 2 8585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00278741
X-RAY DIFFRACTIONf_angle_d0.649211833
X-RAY DIFFRACTIONf_chiral_restr0.0481326
X-RAY DIFFRACTIONf_plane_restr0.00421548
X-RAY DIFFRACTIONf_dihedral_angle_d15.93373269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.210.35441070.29712283X-RAY DIFFRACTION89.45
3.21-3.340.36971430.29832357X-RAY DIFFRACTION90.98
3.34-3.490.3231160.26572469X-RAY DIFFRACTION94.76
3.49-3.680.32521280.23442589X-RAY DIFFRACTION99.38
3.68-3.910.26261300.22562567X-RAY DIFFRACTION98.54
3.91-4.210.29451260.20712607X-RAY DIFFRACTION99.96
4.21-4.630.22591410.17222616X-RAY DIFFRACTION99.78
4.63-5.30.20451630.1742570X-RAY DIFFRACTION98.45
5.3-6.680.26061660.20882621X-RAY DIFFRACTION99.71
6.68-54.390.19351600.17072680X-RAY DIFFRACTION97.49

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more