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

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1tyv
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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TAILSPIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,6171
Polymers59,6171
Non-polymers00
Water4,053225
1
A: TAILSPIKE PROTEIN

A: TAILSPIKE PROTEIN

A: TAILSPIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)178,8503
Polymers178,8503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27910 Å2
ΔGint-108 kcal/mol
Surface area48040 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 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: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 53872 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.055
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 9999 Å / Num. measured all: 203785
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.85 Å / % possible obs: 96.4 % / Rmerge(I) obs: 0.275

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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
Rwork0.181 -
obs0.181 53375
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 0 225 4333
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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