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- PDB-5jj1: Structure of the Immature Procapsid Conformation of P22 Portal Protein -

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Basic information

Entry
Database: PDB / ID: 5jj1
TitleStructure of the Immature Procapsid Conformation of P22 Portal Protein
ComponentsPortal protein
KeywordsVIRAL PROTEIN / portal protein / dodecamer / packaging motor / procapsid
Function / homologyPhage P22-like portal protein / Phage P22-like portal protein / viral DNA genome packaging, headful / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / virion assembly / Portal protein
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLokareddy, R.K. / Cingolani, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA56036 United States
CitationJournal: Nat Commun / Year: 2017
Title: Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation.
Authors: Lokareddy, R.K. / Sankhala, R.S. / Roy, A. / Afonine, P.V. / Motwani, T. / Teschke, C.M. / Parent, K.N. / Cingolani, G.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein


Theoretical massNumber of molelcules
Total (without water)842,91012
Polymers842,91012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100860 Å2
ΔGint-429 kcal/mol
Surface area501450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)316.808, 316.808, 138.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein
Portal protein / Gene product 1 / Gp1 / Head-to-tail connector


Mass: 70242.477 Da / Num. of mol.: 12 / Fragment: UNP residues 1-602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P26744

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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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 5% PEG 8,000, 10 mM Cesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.502
11-H, K, -L20.498
ReflectionResolution: 3.3→50 Å / Num. obs: 206085 / % possible obs: 100 % / Redundancy: 8.8 % / Net I/σ(I): 10.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→14.998 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 37.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3147 1733 1 %RANDOM
Rwork0.295 ---
obs0.2952 173371 85.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→14.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms56570 0 0 0 56570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457794
X-RAY DIFFRACTIONf_angle_d0.99578468
X-RAY DIFFRACTIONf_dihedral_angle_d11.30148234
X-RAY DIFFRACTIONf_chiral_restr0.0558488
X-RAY DIFFRACTIONf_plane_restr0.00810386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3004-3.39640.35011100.262510472X-RAY DIFFRACTION62
3.3964-3.50470.2892790.299411840X-RAY DIFFRACTION71
3.5047-3.62820.34371570.317611971X-RAY DIFFRACTION72
3.6282-3.77130.33221550.297312995X-RAY DIFFRACTION78
3.7713-3.940.3548780.301713101X-RAY DIFFRACTION78
3.94-4.14350.32931720.286613802X-RAY DIFFRACTION83
4.1435-4.3970.3038990.280315015X-RAY DIFFRACTION89
4.397-4.72660.33081890.276515803X-RAY DIFFRACTION94
4.7266-5.18430.29041990.285916289X-RAY DIFFRACTION97
5.1843-5.89430.2831960.303416612X-RAY DIFFRACTION98
5.8943-7.28190.3522020.318816787X-RAY DIFFRACTION99
7.2819-14.99770.28881970.294416951X-RAY DIFFRACTION99

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