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- PDB-2m5s: High-resolution NMR structure and cryo-EM imaging support multipl... -

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Basic information

Entry
Database: PDB / ID: 2m5s
TitleHigh-resolution NMR structure and cryo-EM imaging support multiple functional roles for the accessory I-domain of phage P22 coat protein
ComponentsCoat protein
KeywordsVIRAL PROTEIN / telokin-like domain / extra-density domain / D-loop
Function / homology
Function and homology information


viral procapsid / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #240 / Major capsid protein Gp5 / P22 coat protein - gene protein 5 / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsclosest to the aveerage, model1
AuthorsRizzo, A.A. / Suhanovsky, M.M. / Baker, M.L. / Fraser, L.C.R. / Jones, L.M. / Rempel, D.L. / Gross, M.L. / Chiu, W. / Alexandrescu, A.T. / Teschke, C.M.
CitationJournal: Structure / Year: 2014
Title: Multiple Functional Roles of the Accessory I-Domain of Bacteriophage P22 Coat Protein Revealed by NMR Structure and CryoEM Modeling.
Authors: Rizzo, A.A. / Suhanovsky, M.M. / Baker, M.L. / Fraser, L.C. / Jones, L.M. / Rempel, D.L. / Gross, M.L. / Chiu, W. / Alexandrescu, A.T. / Teschke, C.M.
History
DepositionMar 5, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 2, 2014Group: Database references
Revision 1.3May 1, 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: Coat protein


Theoretical massNumber of molelcules
Total (without water)13,8661
Polymers13,8661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Coat protein / Protein gp5


Mass: 13865.555 Da / Num. of mol.: 1
Fragment: This domain has previously been called the 'extra-density domain' and 'telokin-like domain' in the literature based on cryo-EM models
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: 5, gp5 coat protein / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P26747

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR structure of amino acids 223-345 from P22's coat protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D HNCA
1413D HN(CO)CA
1513D HNCO
1613D HN(CA)CO
1723D CCH-TOCSY
1823D (H)CCH-TOCSY
1913D HNHB
11013D Long-range HNCO
11113D HNHA
11213D 1H-15N TOCSY
11323D 1H-13C NOESY
11413D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-100% 13C; U-100% 15N] protein, 20 mM sodium phosphate, 1% H2O/99% D2O1% H2O/99% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMProtein-1[U-100% 13C; U-100% 15N]1
20 mMSodium Phosphate-21
1.5 mMProtein-3[U-100% 13C; U-100% 15N]2
20 mMSodium Phosphate-42
Sample conditionsIonic strength: 20 / pH: 6.0 / Pressure: ambient / Temperature: 310.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionClassification
ARIA2.3.1peak picking
ARIA/CNS/CCPNmr_Analysisrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: Automated assignment of NOE spectra was carried out using ARIA using floating chirality. CCPNmr Analysis was used to inspect violations and refine the structure for further calculations with ARIA.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 30

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