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- PDB-1clw: TAILSPIKE PROTEIN FROM PHAGE P22, V331A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1clw
TitleTAILSPIKE PROTEIN FROM PHAGE P22, V331A MUTANT
ComponentsTAILSPIKE PROTEIN
KeywordsVIRAL PROTEIN / LATE PROTEIN / VIRUS/VIRAL 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 / OTHER / Resolution: 2 Å
AuthorsSteinbacher, S. / Baxa, U. / Weintraub, A. / Huber, R. / Seckler, R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Mutations improving the folding of phage P22 tailspike protein affect its receptor binding activity.
Authors: Baxa, U. / Steinbacher, S. / Weintraub, A. / Huber, R. / Seckler, R.
History
DepositionMay 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 5, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)59,5891
Polymers59,5891
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TAILSPIKE PROTEIN

A: TAILSPIKE PROTEIN

A: TAILSPIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)178,7663
Polymers178,7663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27750 Å2
ΔGint-113 kcal/mol
Surface area48390 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 / LATE PROTEIN GP9


Mass: 59588.594 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT / Mutation: V331A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: 9 / Production host: Escherichia coli (E. coli) / References: UniProt: P12528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growpH: 10 / Details: pH 10.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 10 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium sulfate1reservoir
20.1 Msodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→8 Å / Num. obs: 40008 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / % possible all: 93.6
Reflection
*PLUS
Num. measured all: 128481 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 93.6 % / Rmerge(I) obs: 0.157

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: 1TSP

1tsp


Resolution: 2→8 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.171 --
obs0.171 39282 99.5 %
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 0 213 4326
Refine LS restraints
Refine-IDTypeDev ideal
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor obs: 0.171 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.6

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