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- PDB-1yq8: PRD1 vertex protein P5 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1yq8
TitlePRD1 vertex protein P5
ComponentsMinor capsid protein
KeywordsVIRAL PROTEIN / beta-spiral beta-jelly-roll
Function / homology
Function and homology information


icosahedral viral capsid, spike
Similarity search - Function
Minor capsid protein. / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5 C-terminal domain superfamily / Bacteriophage PRD1, spike protein P5, C-terminal / Bacteriophage PRD1, P5, spike N-terminal / Bacteriophage PRD1, P5, spike N-terminal / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage PRD1 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMerckel, M.C. / Huiskonen, J.T. / Goldman, A. / Bamford, D.H. / Tuma, R.
CitationJournal: Mol.Cell / Year: 2005
Title: The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture.
Authors: Merckel, M.C. / Huiskonen, J.T. / Bamford, D.H. / Goldman, A. / Tuma, R.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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

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Assembly

Deposited unit
A: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)19,3861
Polymers19,3861
Non-polymers00
Water00
1
A: Minor capsid protein

A: Minor capsid protein

A: Minor capsid protein


Theoretical massNumber of molelcules
Total (without water)58,1583
Polymers58,1583
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area11990 Å2
ΔGint-79 kcal/mol
Surface area19770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.240, 52.240, 234.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological unit is a trimer generated from the chain A in the asymmetric unit by the operations: -Y,X-Y,Z and Y-X,-X,Z

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Components

#1: Protein Minor capsid protein / Protein P5


Mass: 19385.850 Da / Num. of mol.: 1 / Fragment: P5CdelG8, residues 142-340 / Mutation: deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage PRD1 (virus) / Genus: Tectivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P22536

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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: 2.97 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris HCL, MgCl2, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2002
RadiationMonochromator: Confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→44.4 Å / Num. all: 7251 / Num. obs: 7238 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.83 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
CrystalClear 1.3data collection
CrystalClear 1.3data reduction
CNSrefinement
CrystalClearV. 1.3 (MSC/RIGAKU)data reduction
CrystalClearV. 1.3 (MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.4 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3 770 Random
Rwork0.261 --
obs0.261 7238 -
all-7260 -
Refinement stepCycle: LAST / Resolution: 2.6→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 0 0 1354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3

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