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- PDB-2l6r: High resolution NMR structure of gpW (W protein of bacteriophage ... -

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Basic information

Entry
Database: PDB / ID: 2l6r
TitleHigh resolution NMR structure of gpW (W protein of bacteriophage lambda) at acidic pH
ComponentsHead-to-tail joining protein W (GpW) from bacteriophage origin
KeywordsVIRAL PROTEIN / gpW / atom by atom analysis / fast protein folding / downhill protein folding / folding simulations
Function / homology
Function and homology information


viral life cycle / virion component
Similarity search - Function
Head-to-tail joining protein W, gpW / Head-to-tail joining protein W / Head-to-tail joining protein W / Head-to-tail joining protein W superfamily / gpW / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Head completion protein
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, distance geometry
AuthorsSborgi, L. / Verma, A. / Munoz, V. / de Alba, E.
CitationJournal: To be Published
Title: High resolution NMR structure of gpW (W protein of bacteriophage lambda) at acidic pH
Authors: Sborgi, L. / Verma, A. / Munoz, V. / de Alba, E.
History
DepositionNov 24, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Head-to-tail joining protein W (GpW) from bacteriophage origin


Theoretical massNumber of molelcules
Total (without water)6,9891
Polymers6,9891
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)19 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Head-to-tail joining protein W (GpW) from bacteriophage origin


Mass: 6989.052 Da / Num. of mol.: 1 / Fragment: UNP residues 1-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: W / Production host: Escherichia coli (E. coli) / References: UniProt: P68660*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR model structure for atom by atom analysis of gpW unfolding
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
2213D HN(CA)CB
2313D CBCA(CO)NH
2413D C(CO)NH
2513D HNCO
2613D HBHA(CO)NH
2713D H(CCO)NH
2813D 1H-15N NOESY
1924D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N] gpW-1, 20 mM glycine buffer, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] gpW-2, 20 mM glycine buffer, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMgpW-1[U-13C; U-15N]1
1 mMgpW-2[U-13C; U-15N]2
Sample conditionsIonic strength: 0.02 / pH: 3.5 / Pressure: ambient / Temperature: 293.1 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettpeak picking
PIPPGarrettchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
TALOS+structure solution
RefinementMethod: DGSA-distance geometry simulated annealing, distance geometry
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 19

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