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- PDB-2rpi: The NMR structure of the submillisecond folding intermediate of t... -

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Basic information

Entry
Database: PDB / ID: 2rpi
TitleThe NMR structure of the submillisecond folding intermediate of the Thermus thermophilus ribonuclease H
ComponentsRibonuclease H
KeywordsHYDROLASE / submillisecond folding intermediate / Thermus thermophilus ribonuclease H / High-resolution structure / Endonuclease / Magnesium / Metal-binding / Nuclease
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus HB8 (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
AuthorsZhou, Z. / Feng, H. / Bai, Y.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The high-resolution NMR structure of the early folding intermediate of the Thermus thermophilus ribonuclease H
Authors: Zhou, Z. / Feng, H. / Ghirlando, R. / Bai, Y.
History
DepositionMay 16, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 / 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 / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: 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: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)12,8791
Polymers12,8791
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)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribonuclease H / / RNase H


Mass: 12878.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: rnhA, TTHA1556 / Plasmid: pET42b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P29253, ribonuclease H
Sequence detailsTHE RESIDUES 25-45 IN THE DATABASE SEQUENCE (RNH_THET8 P29253) WERE DELETED SINCE THIS IS THE ...THE RESIDUES 25-45 IN THE DATABASE SEQUENCE (RNH_THET8 P29253) WERE DELETED SINCE THIS IS THE INTERMEDIATE STATE OF THE PROTEIN. IN THIS INTERMEDIATE STATE, IT EXCLUDES THE RESIDUES 25-45, BUT STILL FOLDS WELL. ABOUT RESIDUE 17, 67, THESE CONFLICTS ARE BASED ON FOLDING, THERMAL STABILITY AND EXPRESSION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-1H NOESY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D H(CCO)NH
1913D HNHA
11033D (H)CCH-TOCSY
11113D HBHA(CO)NH
11213D 1H-15N NOESY
11333D 1H-13C NOESY
11413D HN(CA)NNH
11513D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-1.2mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
21.0-1.2mM protein, 100% D2O100% D2O
31.0-1.2mM [U-100% 13C] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein[U-100% 13C; U-100% 15N]1
1.0 mMprotein2
1.0 mMprotein[U-100% 13C]3
Sample conditionsIonic strength: 0.1 / pH: 5.2 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Zhengrong and Baxprocessing
NMRPipeDelaglio, Zhengrong and Baxdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
TALOSDelaglio, Zhengrong and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckNMRLaskowski and MacArthurdata analysis
MOLMOLKoradi, Billeter and Wuthrichstructure solution
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Representative conformer: 1

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