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- PDB-1l5i: 30-CONFORMER NMR ENSEMBLE OF THE N-TERMINAL, DNA-BINDING DOMAIN O... -

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Basic information

Entry
Database: PDB / ID: 1l5i
Title30-CONFORMER NMR ENSEMBLE OF THE N-TERMINAL, DNA-BINDING DOMAIN OF THE REPLICATION INITIATION PROTEIN FROM A GEMINIVIRUS (TOMATO YELLOW LEAF CURL VIRUS-SARDINIA)
ComponentsRep protein
KeywordsVIRAL PROTEIN / A+B FOLD / RBD-LIKE FOLD
Function / homology
Function and homology information


endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / host cell nucleus / structural molecule activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
Geminivirus AL1, replication-associated protein / Geminivirus AL1 replication-associated protein, CLV type / Geminivirus AL1 replication-associated protein, catalytic domain / Geminivirus AL1 replication-associated protein, central domain / Geminivirus Rep catalytic domain / Geminivirus rep protein central domain / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replication-associated protein
Similarity search - Component
Biological speciesTomato yellow leaf curl Sardinia virus
MethodSOLUTION NMR / TORSION ANGLE SIMULATED ANHEALING
AuthorsCampos-Olivas, R. / Louis, J.M. / Clerot, D. / Gronenborn, B. / Gronenborn, A.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The structure of a replication initiator unites diverse aspects of nucleic acid metabolism
Authors: Campos-Olivas, R. / Louis, J.M. / Clerot, D. / Gronenborn, B. / Gronenborn, A.M.
History
DepositionMar 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 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: Rep protein


Theoretical massNumber of molelcules
Total (without water)13,5831
Polymers13,5831
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / -
Representative

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Components

#1: Protein Rep protein


Mass: 13583.302 Da / Num. of mol.: 1
Fragment: N-terminal domain (residues 4-121), DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato yellow leaf curl Sardinia virus / Genus: Begomovirus / Gene: Rep / Production host: Escherichia coli (E. coli) / References: UniProt: P27260

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-SEPARATED NOESY
131HNHA
141HNHB
1514D 13C/15N-SEPARATED NOESY
1612D HN(CO)CG AROM
1712D HNCO AROM
1814D 13C,13C NOESY
NMR detailsText: THIS ENTRY CONTAINS THE 30-CONFORMER ENSEMBLE. THE MINIMIZED AVERAGE STRUCTURE OF THIS ENSEMBLE HAS BEEN DEPOSITED UNDER CODE 1L2M, AND IT IS A GOOD REPRESENTATION OF THE 30-CONFORMER ENSEMBLE CONTAINED HERE.

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Sample preparation

Details
Solution-IDContents
10.8-1.0MM [10%-13C;U-99% 15N] REP4-121, SODIUM PHOSPHATE 20MM, NACL 100MM, DTT 1MM
20.8-1.0MM [U-13C;U-99% 15N] REP4-121, SODIUM PHOSPHATE 20MM, NACL 100MM, DTT 1MM
30.8-1.0MM [10%-13C;U-99% 15N] REP4-121, SODIUM PHOSPHATE 20MM, NACL 100MM, DTT 1MM
40.8-1.0MM [U-13C;U-99 15N] REP4-121, SODIUM PHOSPHATE 20MM, NACL 100MM, DTT 1MM
Sample conditionsIonic strength: 0.3M / pH: 6.6 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7504
Bruker DRXBrukerDRX8005

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Processing

NMR software
NameVersionClassification
NMRPipeprocessing
NMRView4.1.1data analysis
TALOSdata analysis
DYANAstructure solution
DYANArefinement
RefinementMethod: TORSION ANGLE SIMULATED ANHEALING / Software ordinal: 1
NMR ensembleConformers submitted total number: 30

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