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- PDB-1yue: Bacteriophage T4 capsid vertex protein gp24 -

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Basic information

Entry
Database: PDB / ID: 1yue
TitleBacteriophage T4 capsid vertex protein gp24
ComponentsHead vertex protein Gp24
KeywordsVIRAL PROTEIN / gp24 / bacteriophage T4 / capsid protein / vertex / bacteriophage / virus / HK97 / MAD
Function / homology
Function and homology information


Seminal Fluid Protein PDC-109 (Domain B) - #40 / hypothetical protein PF0899 fold - #40 / Capsid vertex protein / Major capsid protein Gp23 / Capsid protein, T4-like bacteriophage-like / hypothetical protein PF0899 fold / Seminal Fluid Protein PDC-109 (Domain B) / Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Capsid vertex protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsFokine, A. / Leiman, P.G. / Shneider, M.M. / Ahvazi, B. / Boeshans, K.M. / Steven, A.C. / Black, L.W. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry.
Authors: Fokine, A. / Leiman, P.G. / Shneider, M.M. / Ahvazi, B. / Boeshans, K.M. / Steven, A.C. / Black, L.W. / Mesyanzhinov, V.V. / Rossmann, M.G.
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Head vertex protein Gp24


Theoretical massNumber of molelcules
Total (without water)47,2731
Polymers47,2731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.614, 107.614, 82.636
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Head vertex protein Gp24


Mass: 47273.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 24 / Plasmid: pET-23 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P19896

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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: 3.7 Å3/Da / Density % sol: 0.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES-Na pH 7.5; 10% v/v isopropanol; 0.2 M Sodium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9
SYNCHROTRONAPS 14-BM-D20.9414, 0.9791, 0.9794, 1.088
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 24, 2004
ADSC QUANTUM 3152CCDJun 24, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.94141
30.97911
40.97941
51.0881
ReflectionResolution: 2.9→35 Å / Num. all: 164088 / Num. obs: 11621 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Biso Wilson estimate: 108 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.9→35 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: High values of atomic B factors reflect the disorder of the crystal. The mosaisity was ~1.5 deg
RfactorNum. reflection% reflectionSelection details
Rfree0.3 586 -random
Rwork0.27 ---
all-12169 --
obs-11621 97.7 %-
Solvent computationSolvent model: Flat Model / Bsol: 48.1183 Å2 / ksol: 0.30571 e/Å3
Displacement parametersBiso mean: 108.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.775 Å223.756 Å20 Å2
2--14.775 Å20 Å2
3----29.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 0 0 3028
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.46

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