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- PDB-2hw0: NMR Solution Structure of the nuclease domain from the Replicator... -

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Basic information

Entry
Database: PDB / ID: 2hw0
TitleNMR Solution Structure of the nuclease domain from the Replicator Initiator Protein from porcine circovirus PCV2
ComponentsReplicase
KeywordsHYDROLASE / REPLICATION / alpha+beta
Function / homology
Function and homology information


: / rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus ...: / rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Viral replication-associated protein, N-terminal / Putative viral replication protein / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent helicase Rep / Replication-associated protein
Similarity search - Component
Biological speciesPorcine circovirus 2
MethodSOLUTION NMR / 30 conformers calculated using simulated anhealing in torsion angle space with CYANA2.0 (MODELS 2-31), average structure after CYANA variable target function minimisation (MODEL 1)
Model type detailsminimized average
AuthorsVega-Rocha, S. / Byeon, I.L. / Gronenborn, B. / Gronenborn, A.M. / Campos-Olivas, R.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution structure, divalent metal and DNA binding of the endonuclease domain from the replication initiation protein from porcine circovirus 2
Authors: Vega-Rocha, S. / Byeon, I.L. / Gronenborn, B. / Gronenborn, A.M. / Campos-Olivas, R.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The authors state that the polypeptide purified from E.coli starts with amino acid number ...SEQUENCE The authors state that the polypeptide purified from E.coli starts with amino acid number 2 of the complete protein because there is in vivo processing of the residue Met1. This has been verified by mass spectrometry of the differently labeled samples produced.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replicase


Theoretical massNumber of molelcules
Total (without water)13,2761
Polymers13,2761
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)31 / 300target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein Replicase


Mass: 13275.991 Da / Num. of mol.: 1 / Fragment: residues 2-116 of Rep PCV2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine circovirus 2 / Genus: Circovirus / Gene: rep, ORF1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta (DE3) pLysS
References: UniProt: Q77NR8, UniProt: Q8BB16*PLUS, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
131HNHB
1434D 13C/15N-separated NOESY
1532D HN(CO)CG aromatic
1632D HNCG aromatic
1744D 13C-separated NOESY
1822D 1H-15N HSQC
1921H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM Rep2-116_PCV2 U-10% 13C;U-15N, 20 mM Sodium phosphate, 100mM NaCl, 1mM DTT, 8% D2O8% D2O
20.8mM Rep2-116_PCV2 U-10% 13C;U-15N, 20 mM Sodium phosphate, 100mM NaCl, 1mM DTT, 100% D2O100% D2O
30.8mM Rep2-116_PCV2 U-13C; U-15N, 20 mM Sodium phosphate, 100mM NaCl, 1mM DTT, 8% D2O8% D2O
40.8mM Rep2-116_PCV2 U-13C;U-15N, 20 mM Sodium phosphate, 100mM NaCl, 1mM DTT, 100% D2O100% D2O
Sample conditionsIonic strength: 0.264 / pH: 6.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRView5.0.4Bruce Johnson, One moon scientificdata analysis
CYANA2Peter Guentertstructure solution
NMRPipeXFrank Delaglio, NIHprocessing
TALOSXFrank Delaglio, NIHdata analysis
CYANA2Peter Guentertrefinement
RefinementMethod: 30 conformers calculated using simulated anhealing in torsion angle space with CYANA2.0 (MODELS 2-31), average structure after CYANA variable target function minimisation (MODEL 1)
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 31

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