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- PDB-1qa1: TAILSPIKE PROTEIN, MUTANT V331G -

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Basic information

Entry
Database: PDB / ID: 1qa1
TitleTAILSPIKE PROTEIN, MUTANT V331G
ComponentsTAILSPIKE PROTEIN
KeywordsViral protein/receptor / virus/viral protein / Viral protein-receptor COMPLEX
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
AuthorsBaxa, U. / Steinbacher, S. / 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
DepositionApr 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)59,5751
Polymers59,5751
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)178,7243
Polymers178,7243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27760 Å2
ΔGint-113 kcal/mol
Surface area48350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.9, 120.9, 120.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213

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Components

#1: Protein TAILSPIKE PROTEIN


Mass: 59574.570 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING C-TERMINAL DOMAIN / Mutation: V331G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / 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: 50.22 %
Crystal growTemperature: 274 K / Method: vapor diffusion, hanging drop / pH: 10
Details: VAPOR DIFFUSION, HANGING DROP, 274 K, PH 10.0, 1M AMMONIUM SULPHATE 0.1M NA- PHOSPHATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Mammonium sulfate11
20.1 Msodium phosphate11

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 39183 / % possible obs: 97.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.041
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.09 / % possible all: 88.7
Reflection
*PLUS
Num. obs: 39183 / Num. measured all: 115812
Reflection shell
*PLUS
% possible obs: 88.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MAR345data collection
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER /
RfactorNum. reflection
all0.161 38426
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 0 213 4319
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS

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