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- PDB-1jnb: CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29 -

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Basic information

Entry
Database: PDB / ID: 1jnb
TitleCONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29
ComponentsUPPER COLLAR PROTEIN
KeywordsVIRAL PROTEIN / helix bundle
Function / homology
Function and homology information


viral procapsid / viral portal complex / 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 / Portal protein Gp10 superfamily / Phage Connector (GP10) / 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 / Portal protein Gp10 superfamily / Phage Connector (GP10) / 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, MIR / Resolution: 3.2 Å
AuthorsSimpson, A.A. / Leiman, P.G. / Tao, Y. / He, Y. / Badasso, M.O. / Jardine, P.J. / Anderson, D.L. / Rossmann, M.G.
Citation
Journal: 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
DepositionJul 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74300 Å2
ΔGint-359 kcal/mol
Surface area123970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)177.160, 169.240, 185.440
Angle α, β, γ (deg.)90, 114.1, 90
Int Tables number5
Space group name H-MC121
Detailsbiological unit is dodecamer, as found in crystal ASU

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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 / Plasmid: PPC28D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04332

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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: 2.95 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30-40% MPD, 0.1 M Tris-HCl pH 8.0, 0.05 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
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 14, 1999
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.21→50 Å / Num. all: 78427 / Num. obs: 78035 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 21
Reflection shellResolution: 3.21→3.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.198 / Num. unique all: 2043 / % possible all: 100
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
AMoRE+ DMphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: molecular replacement, MIR
Starting model: low resolution model, based on cryo-EM data

Resolution: 3.2→9 Å
Isotropic thermal model: individual, restrained between neighbours
Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: CNS version 1.0 used for refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.3014 3680 5 %random
Rwork0.2844 ---
all0.36 74252 --
obs0.2866 73153 98.5 %-
Solvent computationSolvent model: solvent mask calculated using atomic coordinates
Displacement parametersBiso mean: 46.9935 Å2
Baniso -1Baniso -2Baniso -3
1--13.598 Å20 Å2-3.231 Å2
2---7.115 Å20 Å2
3---20.713 Å2
Refinement stepCycle: LAST / Resolution: 3.2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25236 0 0 0 25236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_bond_d0.0009
Refine LS restraints NCSNCS model details: restrained - 3 rigid domains per subunit / Rms dev position: 0.03 Å / Weight Biso : 2000 / Weight position: 300
LS refinement shellResolution: 3.2→3.22 Å
RfactorNum. reflection% reflection
Rfree0.3341 73 5 %
Rwork0.2835 1276 -
obs-69473 99.8 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 9 Å / σ(F): 3 / % reflection Rfree: 5 % / Rfactor obs: 0.2844
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shell
*PLUS
Highest resolution: 3.2 Å / % reflection Rfree: 5 %

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