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- PDB-6mnt: CUS-3 coat protein I-domain -

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Basic information

Entry
Database: PDB / ID: 6mnt
TitleCUS-3 coat protein I-domain
ComponentsPutative coat protein
KeywordsVIRAL PROTEIN / anti-parallel beta-barrel
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral capsid / Putative coat protein
Function and homology information
Biological speciesEnterobacteria phage CUS-3 (virus)
MethodSOLUTION NMR / molecular dynamics
AuthorsTripler, T.N. / Kaplan, A.R. / Alexandrescu, A.T. / Teschke, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentR01 GM076661 United States
CitationJournal: To Be Published
Title: CUS-3 and Sf6 coat protein I-domains
Authors: Tripler, T.N. / Kaplan, A.R. / Alexandrescu, A.T. / Teschke, C.M.
History
DepositionOct 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative coat protein


Theoretical massNumber of molelcules
Total (without water)13,2731
Polymers13,2731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative coat protein


Mass: 13272.730 Da / Num. of mol.: 1 / Fragment: I-domain, residues 223-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage CUS-3 (virus) / Gene: ECRS218_0018 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5VW72

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D HN(CA)CB
121isotropic12D 1H-15N HSQC
132isotropic13D HN(CO)CA
142isotropic1HN(CA)CO
152isotropic13D HNCO
161isotropic13D 1H-15N NOESY
172isotropic13D 1H-13C NOESY
183isotropic23D 1H-15N TOCSY
192isotropic13D HBHA(CO)NH
1102isotropic13D (H)CCH-TOCSY
1112isotropic13D CCH-TOCSY
1122isotropic13D 1H-13C NOESY aliphatic
1133isotropic22D DQF-COSY
1143isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.99 mM [U-99% 15N] CUS-3 coat protein I-domain, 20 mM sodium phosphate, 90% H2O/10% D2O15N sample90% H2O/10% D2O
solution21.9 mM [U-99% 15N], U-99% 13C CUS-3 coat protein I-domain, 20 mM sodium phosphate, 90% H2O/10% D2O15N13C sample90% H2O/10% D2O
solution31.9 mM [U-99% 15N] CUS-3 coat protein I-domain, 20 mM sodium phosphate, 100% D2OD20100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.99 mMCUS-3 coat protein I-domain[U-99% 15N]1
20 mMsodium phosphatenatural abundance1
1.9 mMCUS-3 coat protein I-domain[U-99% 15N], U-99% 13C2
20 mMsodium phosphatenatural abundance2
1.9 mMCUS-3 coat protein I-domain[U-99% 15N]3
20 mMsodium phosphatenatural abundance3
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6 / Pressure: 1 atm / Temperature: 298.13 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
FelixAccelrys Software Inc.processing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNMRCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
CcpNMRCCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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