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- PDB-1tyu: STRUCTURE OF TAILSPIKE-PROTEIN -

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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 / metabolic process / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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