[English] 日本語
Yorodumi
- PDB-5iuc: Crystal structure of the GspB siglec domain with sialyl T antigen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iuc
TitleCrystal structure of the GspB siglec domain with sialyl T antigen bound
ComponentsPlatelet binding protein GspB
KeywordsSUGAR BINDING PROTEIN / bacterial adhesin / lectin / immunoglobulin fold / serine-rich repeat
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
Immunoglobulin-like - #4140 / Atypical Rib domain / Atypical Rib domain / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like ...Immunoglobulin-like - #4140 / Atypical Rib domain / Atypical Rib domain / Serine-rich repeat adhesion glycoprotein / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Platelet binding protein GspB
Similarity search - Component
Biological speciesStreptococcus gordonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.253 Å
AuthorsLoukachevitch, L.V. / Fialkowski, K.P. / Wawrzak, Z. / Iverson, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI106987 United States
CitationJournal: PLoS Pathog. / Year: 2011
Title: A structural model for binding of the serine-rich repeat adhesin GspB to host carbohydrate receptors.
Authors: Pyburn, T.M. / Bensing, B.A. / Xiong, Y.Q. / Melancon, B.J. / Tomasiak, T.M. / Ward, N.J. / Yankovskaya, V. / Oliver, K.M. / Cecchini, G. / Sulikowski, G.A. / Tyska, M.J. / Sullam, P.M. / Iverson, T.M.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionApr 13, 2016ID: 4I8E
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Database references
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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_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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Platelet binding protein GspB
B: Platelet binding protein GspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3036
Polymers27,9052
Non-polymers1,3984
Water10,719595
1
A: Platelet binding protein GspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6513
Polymers13,9521
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Platelet binding protein GspB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6513
Polymers13,9521
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.670, 66.547, 55.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-913-

HOH

21A-967-

HOH

31B-906-

HOH

41B-959-

HOH

-
Components

#1: Protein Platelet binding protein GspB / Serine-rich adhesin for platelets / Serine-rich repeat protein GspB


Mass: 13952.391 Da / Num. of mol.: 2 / Fragment: binding region, Siglec domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus gordonii (bacteria) / Gene: gspB / Plasmid: pBG101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q939N5
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 % / Mosaicity: 0.293 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: PEG 3350, NaCl, Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 67016 / % possible obs: 95.8 % / Redundancy: 14.9 % / Biso Wilson estimate: 12.07 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.018 / Rrim(I) all: 0.068 / Χ2: 1.028 / Net I/av σ(I): 35.585 / Net I/σ(I): 13 / Num. measured all: 997601
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.25-1.2914.30.406191.4
1.29-1.3514.80.32194.1
1.35-1.4114.90.264194.4
1.41-1.4815.10.197195.1
1.48-1.5715.20.145195.7
1.57-1.715.20.111195.9
1.7-1.8715.20.088196.8
1.87-2.1415.10.073197.3
2.14-2.6914.90.065198.2
2.69-3014.20.048198.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QC5

3qc5


Resolution: 1.253→29.859 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.36
RfactorNum. reflection% reflection
Rfree0.1778 3212 4.8 %
Rwork0.1556 --
obs0.1567 66965 95.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.33 Å2 / Biso mean: 16.4634 Å2 / Biso min: 5.75 Å2
Refinement stepCycle: final / Resolution: 1.253→29.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 178 595 2701
Biso mean--14.63 27.15 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132162
X-RAY DIFFRACTIONf_angle_d1.5072946
X-RAY DIFFRACTIONf_chiral_restr0.079352
X-RAY DIFFRACTIONf_plane_restr0.007379
X-RAY DIFFRACTIONf_dihedral_angle_d11.017796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.253-1.27120.26821200.22762449256986
1.2712-1.29110.27281520.21432658281094
1.2911-1.31220.25641230.20982719284294
1.3122-1.33490.23121330.20092680281393
1.3349-1.35910.19541430.19332697284094
1.3591-1.38530.20681320.18732703283595
1.3853-1.41360.19921350.18962720285594
1.4136-1.44430.22981570.18232710286795
1.4443-1.47790.21971360.18082723285995
1.4779-1.51490.19771420.17292736287895
1.5149-1.55580.19621160.17412772288896
1.5558-1.60160.18531520.16472714286696
1.6016-1.65330.20851350.16962780291596
1.6533-1.71240.17541150.16122807292296
1.7124-1.78090.20251580.16472777293597
1.7809-1.8620.17421520.16412802295497
1.862-1.96010.17731450.15132817296297
1.9601-2.08290.1581630.14762807297097
2.0829-2.24370.16431220.13972878300098
2.2437-2.46930.16151290.14932882301198
2.4693-2.82640.17461510.14942909306098
2.8264-3.56010.16421590.14212933309299
3.5601-29.86760.15581420.13773080322298

+
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://pdbjlvh1.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