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- PDB-1tsp: CRYSTAL STRUCTURE OF P22 TAILSPIKE PROTEIN: INTERDIGITATED SUBUNI... -

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Basic information

Entry
Database: PDB / ID: 1tsp
TitleCRYSTAL STRUCTURE OF P22 TAILSPIKE PROTEIN: INTERDIGITATED SUBUNITS IN A THERMOSTABLE TRIMER
ComponentsTAILSPIKE-PROTEIN
KeywordsLATE PROTEIN
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: 2 Å
AuthorsSteinbacher, S. / Seckler, R. / Miller, S. / Steipe, B. / Huber, R. / Reinemer, P.
CitationJournal: 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
DepositionJun 16, 1994Processing site: BNL
Revision 1.0Sep 15, 1995Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAILSPIKE-PROTEIN


Theoretical massNumber of molelcules
Total (without water)60,2651
Polymers60,2651
Non-polymers00
Water3,927218
1
A: TAILSPIKE-PROTEIN

A: TAILSPIKE-PROTEIN

A: TAILSPIKE-PROTEIN


Theoretical massNumber of molelcules
Total (without water)180,7963
Polymers180,7963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27640 Å2
ΔGint-105 kcal/mol
Surface area48840 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 / TSP


Mass: 60265.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / References: UniProt: P12528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / pH: 10
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium sulfate1reservoir
20.1 Msodium phosphate1reservoir
310 mg/mlprotein1drop
410 mMHEPES1drop
51.5 Mammonium sulfate1drop
60.1 Msodium phosphate1drop

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(I): 2.5 /
RfactorNum. reflection
Rwork0.184 -
obs0.184 34670
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 0 218 4339
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.7
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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