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- PDB-1ijg: Structure of the Bacteriophage phi29 Head-Tail Connector Protein -

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Basic information

Entry
Database: PDB / ID: 1ijg
TitleStructure of the Bacteriophage phi29 Head-Tail Connector Protein
ComponentsUPPER COLLAR PROTEIN
KeywordsVIRAL PROTEIN / alpha-helical bundle / RNA binding motif
Function / homology
Function and homology information


viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / RNA binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Phage Connector (GP10) / Portal protein Gp10 superfamily / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel ...Serum Albumin; Chain A, Domain 1 - #30 / Upper collar protein gp10 (connector protein) fold / Upper collar protein gp10 (connector protein) / Bacteriophage PHI-29 conector. Domain 3 / Portal protein Gp10 / Phage Connector (GP10) / Portal protein Gp10 superfamily / Crambin / Serum Albumin; Chain A, Domain 1 / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSimpson, A.A. / Leiman, P.G. / Tao, Y. / He, Y. / Badasso, M. / Jardine, P.J. / Anderson, D.L. / Rossmann, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure determination of the head-tail connector of bacteriophage phi29.
Authors: Simpson, A.A. / Leiman, P.G. / Tao, Y. / He, Y. / Badasso, M.O. / Jardine, P.J. / Anderson, D.L. / Rossmann, M.G.
History
DepositionApr 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPPER COLLAR PROTEIN
B: UPPER COLLAR PROTEIN
C: UPPER COLLAR PROTEIN
D: UPPER COLLAR PROTEIN
E: UPPER COLLAR PROTEIN
F: UPPER COLLAR PROTEIN
G: UPPER COLLAR PROTEIN
H: UPPER COLLAR PROTEIN
I: UPPER COLLAR PROTEIN
J: UPPER COLLAR PROTEIN
K: UPPER COLLAR PROTEIN
L: UPPER COLLAR PROTEIN


Theoretical massNumber of molelcules
Total (without water)431,00812
Polymers431,00812
Non-polymers00
Water13,565753
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70160 Å2
ΔGint-379 kcal/mol
Surface area121290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.753, 171.568, 184.707
Angle α, β, γ (deg.)90.00, 112.21, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dodecamer luckily comprising the asymmetric unit.

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Components

#1: Protein
UPPER COLLAR PROTEIN / CONNECTOR PROTEIN


Mass: 35917.293 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: 10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04332
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 3.56 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, calcium cloride, tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
136-40 %MPD11
20.05 M11CaCl2
30.1 MTris-HCl11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 1999 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 112772 / Num. obs: 110311 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 28.9
Reflection shellResolution: 2.9→2.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.333 / % possible all: 99.6
Reflection
*PLUS
Redundancy: 3.54 %
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FOU

1fou


Resolution: 2.9→500 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2500 2.27 %Random
Rwork0.224 ---
all0.225 112772 --
obs0.225 110311 97.8 %-
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1--10.282 Å20 Å2-9.466 Å2
2---5.561 Å20 Å2
3---15.843 Å2
Refine analyzeLuzzati coordinate error obs: 0.363 Å
Refinement stepCycle: LAST / Resolution: 2.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25224 0 0 753 25977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.21585
X-RAY DIFFRACTIONc_bond_d0.007638
LS refinement shellResolution: 2.9→2.92 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.29 56 2.5 %
Rwork0.324 2183 -
obs-2239 99.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 2.27 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 54.2 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.29 / % reflection Rfree: 2.5 % / Rfactor Rwork: 0.324

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