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- PDB-2mdp: The bacteriophage T7 encoded inhibitor (gp1.2) of E. coli dGTP tr... -

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Basic information

Entry
Database: PDB / ID: 2mdp
TitleThe bacteriophage T7 encoded inhibitor (gp1.2) of E. coli dGTP triphosphohydrolase
ComponentsGene 1.2 protein
KeywordsVIRAL PROTEIN / dNTPase inhibitor
Function / homologyInhibitor of dGTPase, bacteriophage T7-like / Bacteriophage T7-like, gene 1.2 / DNA replication / Inhibitor of dGTPase
Function and homology information
Biological speciesEnterobacteria phage T7 (virus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMueller, G.A. / London, R.E.
CitationJournal: To be Published
Title: The bacteriophage T7 encoded inhibitor (gp1.2) of E. coli dGTP triphosphohydrolase
Authors: Singh, D. / Mueller, G.A. / Smith, C.E. / Krahn, J.M. / London, R.E. / Schaaper, R.M.
History
DepositionSep 16, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
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: Gene 1.2 protein


Theoretical massNumber of molelcules
Total (without water)10,2031
Polymers10,2031
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)10 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Gene 1.2 protein


Mass: 10203.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Gene: 1.2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03780

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D C(CO)NH
1613D (H)CCH-TOCSY
1713D H(CCO)NH
1813D HN(CA)CB
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11112D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-100% 13C; U-100% 15N] protein, 46 mM sodium chloride, 1 mM potassium chloride, 1.4 mM sodium phosphate, 0.05 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
20.2 mM [U-100% 13C; U-100% 15N] protein, 46 mM sodium chloride, 1 mM potassium chloride, 1.4 mM sodium phosphate, 0.05 mM potassium phosphate, 50 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMentity-1[U-100% 13C; U-100% 15N]1
46 mMsodium chloride-21
1 mMpotassium chloride-31
1.4 mMsodium phosphate-41
0.05 mMpotassium phosphate-51
0.2 mMentity-6[U-100% 13C; U-100% 15N]2
46 mMsodium chloride-72
1 mMpotassium chloride-82
1.4 mMsodium phosphate-92
0.05 mMpotassium phosphate-102
50 mg/mLPf1 phage-112
Sample conditionsIonic strength: 69.8 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CS-ROSETTAShen, Vernon, Baker and Baxdata analysis
CYANAHerrmann, Guntert and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement in explicit solvent
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 10

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