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- PDB-1lkt: CRYSTAL STRUCTURE OF THE HEAD-BINDING DOMAIN OF PHAGE P22 TAILSPI... -

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Basic information

Entry
Database: PDB / ID: 1lkt
TitleCRYSTAL STRUCTURE OF THE HEAD-BINDING DOMAIN OF PHAGE P22 TAILSPIKE PROTEIN
ComponentsTAILSPIKE PROTEIN
KeywordsVIRAL PROTEIN / VIRUS PROTEIN / SALMONELLA PHAGE P22 / TELLUROMETHIONINE / LATE 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
Tailspike Protein; Chain / Phage P22 tailspike-like, N-terminal domain / 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 / Pectin lyase fold/virulence factor / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.6 Å
AuthorsSteinbacher, S.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Phage P22 tailspike protein: crystal structure of the head-binding domain at 2.3 A, fully refined structure of the endorhamnosidase at 1.56 A resolution, and the molecular basis of O-antigen ...Title: Phage P22 tailspike protein: crystal structure of the head-binding domain at 2.3 A, fully refined structure of the endorhamnosidase at 1.56 A resolution, and the molecular basis of O-antigen recognition and cleavage.
Authors: Steinbacher, S. / Miller, S. / Baxa, U. / Budisa, N. / Weintraub, A. / Seckler, R. / Huber, R.
History
DepositionOct 17, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

Downloads & links

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Assembly

Deposited unit
A: TAILSPIKE PROTEIN
B: TAILSPIKE PROTEIN
C: TAILSPIKE PROTEIN
D: TAILSPIKE PROTEIN
E: TAILSPIKE PROTEIN
F: TAILSPIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)67,8476
Polymers67,8476
Non-polymers00
Water7,782432
1
A: TAILSPIKE PROTEIN
B: TAILSPIKE PROTEIN
C: TAILSPIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,9233
Polymers33,9233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-40 kcal/mol
Surface area13820 Å2
MethodPISA
2
D: TAILSPIKE PROTEIN
E: TAILSPIKE PROTEIN
F: TAILSPIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,9233
Polymers33,9233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-41 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.300, 82.100, 73.800
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.873199, -0.24515, 0.421218), (-0.487336, -0.429977, 0.760016), (-0.005204, -0.86892, -0.494925)-17.1903, -4.2404, 108.7008
2given(0.871423, -0.490106, -0.020434), (-0.240763, -0.391047, -0.888322), (0.427381, 0.779024, -0.458766)14.7742, 88.796, 61.2063
3given(0.997753, -0.061272, 0.027092), (0.064134, 0.990474, -0.121856), (-0.019367, 0.12332, 0.992178)28.2716, 1.584, 35.1945
4given(0.862434, -0.21541, 0.458047), (-0.503624, -0.274526, 0.819145), (-0.050706, -0.937141, -0.345246)21.647, 6.7719, 88.9802
5given(0.850584, -0.524546, 0.036864), (-0.255363, -0.473335, -0.843056), (0.459671, 0.707676, -0.536561)38.0834, 49.7558, 58.193

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Components

#1: Protein
TAILSPIKE PROTEIN / LATE PROTEIN GP9 / TAIL PROTEIN / TSP


Mass: 11307.753 Da / Num. of mol.: 6 / Fragment: HEAD-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Cell line: BL21 / Organ: TAIL / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P12528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 51.89 %
Crystal growpH: 6.6 / Details: 20% PEG 8K, 0.2 M MGCL2, 0.1 M BIS-TRIS, PH 6.6
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(w/v)PEG80001reservoir
20.2 M1reservoirMgCl2
30.1 MBis-Tris-HCl1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 20822 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.6→2.65 Å / Rmerge(I) obs: 0.298 / % possible all: 72.2
Reflection
*PLUS
Num. measured all: 48766
Reflection shell
*PLUS
% possible obs: 72.2 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.199 --
obs0.199 28206 96.5 %
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 0 432 5214
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.55
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.342
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 18825 / Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.49
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d

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