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- PDB-2cps: SOLUTION NMR STRUCTURES OF THE MAJOR COAT PROTEIN OF FILAMENTOUS ... -

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Entry
Database: PDB / ID: 2cps
TitleSOLUTION NMR STRUCTURES OF THE MAJOR COAT PROTEIN OF FILAMENTOUS BACTERIOPHAGE M13 SOLUBILIZED IN SODIUM DODECYL SULPHATE MICELLES, 25 LOWEST ENERGY STRUCTURES
ComponentsM13 MAJOR COAT PROTEIN
KeywordsVIRAL PROTEIN / MAJOR COAT PROTEIN / BACTERIOPHAGE M13 / ASSEMBLY / MICELLE / MEMBRANE
Function / homology
Function and homology information


helical viral capsid / host cell plasma membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage M13 (virus)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING, THIS VERSION OF X-PLOR WAS EXTENDED FOR FLOATING CHIRALITY
AuthorsPapavoine, C.H.M. / Christiaans, B.E.C. / Folmer, R.H.A. / Konings, R.N.H. / Hilbers, C.W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Solution structure of the M13 major coat protein in detergent micelles: a basis for a model of phage assembly involving specific residues.
Authors: Papavoine, C.H. / Christiaans, B.E. / Folmer, R.H. / Konings, R.N. / Hilbers, C.W.
#1: Journal: Biochemistry / Year: 1997
Title: Backbone Dynamics of the Major Coat Protein of Bacteriophage M13 in Detergent Micelles by 15N Nuclear Magnetic Resonance Relaxation Measurements Using the Model-Free Approach and Reduced Spectral Density Mapping
Authors: Papavoine, C.H. / Remerowski, M.L. / Horstink, L.M. / Konings, R.N. / Hilbers, C.W. / Van De Ven, F.J.
#2: Journal: Eur.J.Biochem. / Year: 1995
Title: NMR Studies of the Major Coat Protein of Bacteriophage M13. Structural Information of Gviiip in Dodecylphosphocholine Micelles
Authors: Papavoine, C.H. / Aelen, J.M. / Konings, R.N. / Hilbers, C.W. / Van De Ven, F.J.
#3: Journal: Biochemistry / Year: 1994
Title: Location of M13 Coat Protein in Sodium Dodecyl Sulfate Micelles as Determined by NMR
Authors: Papavoine, C.H. / Konings, R.N. / Hilbers, C.W. / Van De Ven, F.J.
#4: Journal: Biochemistry / Year: 1993
Title: Assignment of 1H, 15N, and Backbone 13C Resonances in Detergent-Solubilized M13 Coat Protein Via Multinuclear Multidimensional NMR: A Model for the Coat Protein Monomer
Authors: Van De Ven, F.J. / Van Os, J.W. / Aelen, J.M. / Wymenga, S.S. / Remerowski, M.L. / Konings, R.N. / Hilbers, C.W.
History
DepositionApr 16, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: M13 MAJOR COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)5,2431
Polymers5,2431
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)25 / 80LOWEST ENERGY, DISTANCE RESTRAINTS SMALLER THAN 0.5 A, DIHEDRAL VIOLATIONS SMALLER THAN 5 DEGREES
Representative

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Components

#1: Protein/peptide M13 MAJOR COAT PROTEIN / M13 GENE-VIII-PROTEIN OR M13 GVIIIP


Mass: 5243.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Genus: Inovirus / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P69541

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131NOESY
141NOESY-HMQC (15N AND 13C)
151TOCSY-HMQC (15N)
161(H)CCH-TOCSY
171ROESY-GHSQC
181HMQC-NOESY-GHSQC
191HMQC-J
1101HNHA
1111HACACB-COSY
1121HNHB
1131HSQC(3J CGN)
1141HSQC(3JCGC')
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N -LABELED M13 COAT PROTEIN SOLUBILIZED IN DEUTERATED SODIUM DODECYL SULPHATE MICELLES (CONCENTRATION COAT PROTEIN/SDS = 1:250)

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Sample preparation

DetailsContents: H2O
Sample conditionspH: 4.9 / Temperature: 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY4001
Bruker AMBrukerAM5002
Bruker AMXBrukerAMX6003

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING, THIS VERSION OF X-PLOR WAS EXTENDED FOR FLOATING CHIRALITY
Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY, DISTANCE RESTRAINTS SMALLER THAN 0.5 A, DIHEDRAL VIOLATIONS SMALLER THAN 5 DEGREES
Conformers calculated total number: 80 / Conformers submitted total number: 25

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