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- PDB-5lgm: Gp5.7 mutant L42A -

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Basic information

Entry
Database: PDB / ID: 5lgm
TitleGp5.7 mutant L42A
ComponentsFusion protein 5.5/5.7
KeywordsTRANSCRIPTION / Transcription effector / anti-sigma effector
Function / homologyProtein suppressor of silencing, bacteriophage T7 / Bacteriophage T7, gene 5.5 / viral translational frameshifting / Fusion protein 5.5/5.7
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
MethodSOLUTION NMR / distance geometry / simulated annealing
AuthorsLiu, B. / Matthews, S.
Citation
#1: Journal: Nucleic Acids Res. / Year: 2014
Title: A bacteriophage transcription regulator inhibits bacterial transcription initiation by sigma factor displacement.
Authors: Liu, B. / Shadrin, A. / Sheppard, C. / Mekler, V. / Xu, Y. / Severinov, K. / Matthews, S. / Wigneshweraraj, S.
History
DepositionJul 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1May 15, 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

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Assembly

Deposited unit
A: Fusion protein 5.5/5.7


Theoretical massNumber of molelcules
Total (without water)7,3791
Polymers7,3791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4070 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Fusion protein 5.5/5.7


Mass: 7379.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Gene: 5.5
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P03787

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D (H)CCH-TOCSY
171isotropic13D H(CCO)NH
191isotropic23D 1H-15N NOESY
181isotropic23D 1H-13C NOESY
1101isotropic23D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 300 mM NA sodium chloride, 50 mM NA sodium phosphate, 90% H2O/10% D2O
Label: 15N_13C_gp5.7 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 mMsodium chlorideNA1
50 mMsodium phosphateNA1
Sample conditionsIonic strength: na Not defined / Label: condition1 / pH: 6 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
Refinement
MethodSoftware ordinal
distance geometry1
simulated annealing2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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