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- PDB-1zae: Solution structure of the functional domain of phi29 replication ... -

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Basic information

Entry
Database: PDB / ID: 1zae
TitleSolution structure of the functional domain of phi29 replication organizer p16.7c
ComponentsEarly protein GP16.7
KeywordsDNA BINDING PROTEIN / phi-29 replication / nonspecific DNA binding protein / helical dimer
Function / homology
Function and homology information


viral DNA genome replication / host cell membrane / DNA replication / host cell plasma membrane / DNA binding / membrane
Similarity search - Function
Phage phi29 replication organiser protein p16.7-like / Bacteriophage DNA replication protein Gp16.7 / Bacteriophage DNA replication protein Gp16.7 superfamily / Bacteriophage phi-29 early protein GP16.7 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA replication protein 16.7
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsAsensio, J.L. / Albert, A. / Munoz-Espin, D. / Gonzalez, C. / Hermoso, J. / Villar, L. / Jimenez-Barbero, J. / Salas, M. / Meijer, W.J.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of the functional domain of phi29 replication organizer: insights into oligomerization and dna binding
Authors: Asensio, J.L. / Albert, A. / Munoz-Espin, D. / Gonzalez, C. / Hermoso, J. / Villar, L. / Jimenez-Barbero, J. / Salas, M. / Meijer, W.J.J.
History
DepositionApr 6, 2005Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 19, 2005ID: 1Z61
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Early protein GP16.7
B: Early protein GP16.7


Theoretical massNumber of molelcules
Total (without water)16,6452
Polymers16,6452
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)25 / 25all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein Early protein GP16.7 / p16.7c


Mass: 8322.401 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P16517

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1400UM P16.7c, 200MM NACL, 10MM SODIUM PHOSPHATE BUFFER, 4MM DTT AT PH 5.090% H2O/10% D2O
2800UM P16.7c, 200MM NACL, 10MM SODIUM PHOSPHATE BUFFER, 4MM DTT AT PH 5.090% H2O/10% D2O
3400UM P16.7c, 200MM NACL, 10MM SODIUM PHOSPHATE BUFFER, 4MM DTT AT PH 7.090% H2O/10% D2O
4800UM P16.7c, 200MM NACL, 10MM SODIUM PHOSPHATE BUFFER, 4MM DTT AT PH 7.090% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200mM NACL 5 ambient 308 K
2200mM NACL 7 ambient 308 K
3200mM NACL 5 ambient 303 K
4200mM NACL 5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.4Gunter, P.refinement
Amber5Kollman, P.refinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 25 / Conformers submitted total number: 25

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