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- PDB-1qhk: N-TERMINAL DOMAIN OF SACCHAROMYCES CEREVISIAE RNASE HI REVEALS A ... -

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Basic information

Entry
Database: PDB / ID: 1qhk
TitleN-TERMINAL DOMAIN OF SACCHAROMYCES CEREVISIAE RNASE HI REVEALS A FOLD WITH A RESEMBLANCE TO THE N-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L9
ComponentsPROTEIN (RIBONUCLEASE HI)
KeywordsHYDROLASE / RIBONUCLEASE HI N-TERMINAL DOMAIN
Function / homology
Function and homology information


DNA replication, removal of RNA primer / RNA catabolic process / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / nucleus / cytoplasm
Similarity search - Function
Ribonuclease H1, N-terminal domain / Ribonuclease H1, eukaryote / Ribonuclease HI; Chain A / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / Ribosomal protein L9/RNase H1, N-terminal / RNase H / RNase H type-1 domain profile. ...Ribonuclease H1, N-terminal domain / Ribonuclease H1, eukaryote / Ribonuclease HI; Chain A / Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Ribonuclease H1 N-terminal domain / : / Ribosomal protein L9/RNase H1, N-terminal / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsEvans, S.P. / Bycroft, M.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: NMR structure of the N-terminal domain of Saccharomyces cerevisiae RNase HI reveals a fold with a strong resemblance to the N-terminal domain of ribosomal protein L9.
Authors: Evans, S.P. / Bycroft, M.
#1: Journal: Nucleic Acids Res. / Year: 1994
Title: Eukaryotic RNase H Shares a Conserved Domain with Caulimovirus Proteins that Facilitate Translation of Polycistronic RNA
Authors: Mushegian, A.R. / Edskes, H.K. / Koonin, E.V.
History
DepositionMay 17, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (RIBONUCLEASE HI)


Theoretical massNumber of molelcules
Total (without water)5,3811
Polymers5,3811
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 / 200LEAST RESTRAINT VIOLATION
RepresentativeModel #14

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Components

#1: Protein/peptide PROTEIN (RIBONUCLEASE HI) / E.C.3.1.26.4 / RNASE HI


Mass: 5380.938 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)C41 / References: UniProt: Q04740, ribonuclease H

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HBHA (CO)NH
151CBCA(CO)NH
161HN(CA)CB
171(H)CCH-TOCSY
181HNHA
191HNHB

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Sample preparation

DetailsContents: ACETATE BUFFER (50 MM)
Sample conditionspH: 3.6 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 200 / Conformers submitted total number: 20

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