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- PDB-7by7: Bacteriophage SPO1 protein Gp46 -

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Basic information

Entry
Database: PDB / ID: 7by7
TitleBacteriophage SPO1 protein Gp46
ComponentsPutative gene 46 protein
KeywordsANTIMICROBIAL PROTEIN / HU / Malaria / Mycobacterium / Bacilius / Broad spectrum HU inhibitor
Function / homologyPutative gene 46 protein
Function and homology information
Biological speciesBacillus phage SP01 (virus)
MethodSOLUTION NMR / simulated annealing / distance geometry
AuthorsLiu, B. / Zhang, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins
Authors: Zhang, P. / Zhao, X. / Wang, Y. / Du, K. / Wang, Z. / Yu, J. / Chang, G. / Matthews, S. / Wang, H. / Liu, B.
History
DepositionApr 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative gene 46 protein


Theoretical massNumber of molelcules
Total (without water)8,9981
Polymers8,9981
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4880 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative gene 46 protein /


Mass: 8998.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SP01 (virus) / Gene: 46 / Production host: Escherichia coli (E. coli) / References: UniProt: O48400

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HN(CA)CO
151isotropic13D HNCO
161isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-13C NOESY
1101isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 300 mM sodium chloride, 50 mM potassium phosphate, 1 mM TCEP, 90% H2O/10% D2O
Label: 15N_13C sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 mMsodium chloridenatural abundance1
50 mMpotassium phosphatenatural abundance1
1 mMTCEPnatural abundance1
Sample conditionsIonic strength: 350 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 300 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
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
Refinement
MethodSoftware ordinal
simulated annealing1
distance geometry2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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