[English] 日本語
Yorodumi
- PDB-1tyu: STRUCTURE OF TAILSPIKE-PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tyu
TitleSTRUCTURE OF TAILSPIKE-PROTEIN
ComponentsTAILSPIKE PROTEIN
KeywordsVIRAL ADHESION PROTEIN / COMPLEX / RECEPTOR / ENDOGLYCOSIDASE CARBOHYDRATE / CELL RECEPTOR / RECOGNITION / BINDING PROTEIN LIPOPOLYSACCHARIDE
Function / homology
Function and homology information


endo-1,3-alpha-L-rhamnosidase activity / symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide / virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / symbiont entry into host / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell
Similarity search - Function
Pectate Lyase C-like - #20 / P22 tailspike C-terminal domain / Salmonella phage P22 tail-spike / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Autotransporter, pectate lyase C-like domain superfamily / Pectate Lyase C-like / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSteinbacher, S. / Huber, R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors.
Authors: Steinbacher, S. / Baxa, U. / Miller, S. / Weintraub, A. / Seckler, R. / Huber, R.
#1: Journal: Biophys.J. / Year: 1996
Title: Interactions of Phage P22 Tails with Their Cellular Receptor, Salmonella O-Antigen Polysaccharide
Authors: Baxa, U. / Steinbacher, S. / Miller, S. / Weintraub, A. / Huber, R. / Seckler, R.
#2: Journal: Science / Year: 1994
Title: Crystal Structure of P22 Tailspike Protein: Interdigitated Subunits in a Thermostable Trimer
Authors: Steinbacher, S. / Seckler, R. / Miller, S. / Steipe, B. / Huber, R. / Reinemer, P.
History
DepositionJul 26, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / 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_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TAILSPIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8362
Polymers59,6171
Non-polymers1,2191
Water3,855214
1
A: TAILSPIKE PROTEIN
hetero molecules

A: TAILSPIKE PROTEIN
hetero molecules

A: TAILSPIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,5076
Polymers178,8503
Non-polymers3,6573
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area35970 Å2
ΔGint-3 kcal/mol
Surface area46930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.900, 120.900, 120.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein TAILSPIKE PROTEIN / TAILSPIKE ENDORHAMNOSIDASE


Mass: 59616.648 Da / Num. of mol.: 1
Fragment: RESIDUES 109-666 LACKING THE N-TERMINAL, HEAD-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: PHAGE P22 GENE 9 / Gene (production host): PHAGE P22 GENE 9 / Production host: Escherichia coli (E. coli) / References: UniProt: P12528
#2: Polysaccharide alpha-D-galactopyranose-(1-2)-[alpha-D-Tyvelopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L- ...alpha-D-galactopyranose-(1-2)-[alpha-D-Tyvelopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-alpha-D-galactopyranose-(1-2)-[alpha-D-Tyvelopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose


Type: oligosaccharide / Mass: 1219.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-2[DTyva1-3]DManpa1-4LRhapa1-3DGalpa1-2[DTyva1-3]DManpa1-4LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2211m-1a_1-5][a1122h-1a_1-5][a2112h-1a_1-5][a1d22m-1a_1-5]/1-2-3-1-2-3-4-4/a4-b1_b2-c1_b3-h1_c3-d1_d4-e1_e2-f1_e3-g1WURCSPDB2Glycan 1.1.0
[][a-L-Rhap]{[(4+1)][a-D-Manp]{[(2+1)][a-D-Galp]{[(3+1)][a-L-Rhap]{[(4+1)][a-D-Manp]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-3-deoxy-Rhap]{}}}}[(3+1)][a-D-3-deoxy-Rhap]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growpH: 7.5
Details: COMPLEX FORMED BY SOAKING WITH 2MM OCTASACCHARIDE FROM SALMONELLA ENTERITIDIS AT PH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 10 / Method: vapor diffusion, hanging drop
Details: drop contained 0.005 ml of drop solution and 0.003 ml of precipitant
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMHEPES1drop
31.5 Mammonium sulfate1dropprecipitant
40.1 Msodium phosphate1dropprecipitant
51.0 Mammonium sulfate1reservoir
60.1 Msodium phosphate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 51290 / % possible obs: 93.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 9999 Å / Num. measured all: 276996
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 18.5 Å / % possible obs: 36.5 % / Rmerge(I) obs: 0.293

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.184 -
obs0.184 50712
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 83 214 4412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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