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- PDB-2ltf: The solution structure of Phage P2 gpX -

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Basic information

Entry
Database: PDB / ID: 2ltf
TitleThe solution structure of Phage P2 gpX
ComponentsTail protein X
KeywordsVIRAL PROTEIN / LysM / phage tail
Function / homologyPhage Tail Protein X-like / Phage Tail Protein X / virus tail, baseplate / Baseplate protein X
Function and homology information
Biological speciesEnterobacteria phage P2 (virus)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model 1
AuthorsMaxwell, K.L. / Bona, D. / Chang, T.L. / Edwards, A.M. / Davidson, A.R.
CitationJournal: To be Published
Title: Structural characterization of the phage P2 baseplate
Authors: Maxwell, K.L. / Hassanabad, M.F. / Chang, T. / Pirani, N. / Paul, V.D. / Bona, D. / Edwards, A.M. / Davidson, A.R.
History
DepositionMay 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
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: Tail protein X


Theoretical massNumber of molelcules
Total (without water)7,5921
Polymers7,5921
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Tail protein X / GpX


Mass: 7591.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P2 (virus) / Gene: X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P51772

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HNCO
1412D 1H-15N HSQC
1513D 1H-15N NOESY
1613D H(CCO)NH
1713D C(CO)NH
1812D 1H-13C HSQC
1923D 1H-13C NOESY aliphatic
11022D 1H-13C HSQC aliphatic
11123D 1H-13C NOESY aromatic
11222D 1H-13C HSQC aromatic
11313D 1H-13C NOESY aliphatic
11413D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] P2 gpX, 25 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM [U-100% 13C; U-100% 15N] P2 gpX, 25 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMP2 gpX-1[U-100% 13C; U-100% 15N]1
25 mMsodium phosphate-21
200 mMsodium chloride-31
2 mMDTT-41
1.1 mMP2 gpX-5[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-62
200 mMsodium chloride-72
2 mMDTT-82
Sample conditionsIonic strength: 200 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 1144 / NOE long range total count: 307 / NOE medium range total count: 264 / NOE sequential total count: 573
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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