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- PDB-2kw4: Solution NMR Structure of the Holo Form of a Ribonuclease H domai... -

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Basic information

Entry
Database: PDB / ID: 2kw4
TitleSolution NMR Structure of the Holo Form of a Ribonuclease H domain from D.hafniense, Northeast Structural Genomics Consortium Target DhR1A
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / Target DhR1A / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


RNA-DNA hybrid ribonuclease activity / nucleic acid binding
Similarity search - Function
Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / RNase H / Ribonuclease H domain / RNase H type-1 domain profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily ...Ribonuclease H1, N-terminal / Ribonuclease H1, N-terminal domain superfamily / Caulimovirus viroplasmin / Ribonuclease H-like superfamily/Ribonuclease H / Ribosomal protein L9/RNase H1, N-terminal / 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
RNase H type-1 domain-containing protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsMills, J.L. / Eletsky, A. / Hua, J. / Belote, R.L. / Buchwald, W.A. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. ...Mills, J.L. / Eletsky, A. / Hua, J. / Belote, R.L. / Buchwald, W.A. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target DhR1A
Authors: Mills, J.L. / Eletsky, A. / Hua, J. / Belote, R.L. / Buchwald, W.A. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionMar 31, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7172
Polymers16,6931
Non-polymers241
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Uncharacterized protein


Mass: 16692.633 Da / Num. of mol.: 1 / Fragment: RIBONUCLEASE H domain residues 69-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: Y51 / Gene: DSY1790 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24WL3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.89 mM [U-100% 13C; U-100% 15N] DhR1A, 150 mM MAGNESIUM Chloride, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 90 % H2O, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.89 mMDhR1A-1[U-100% 13C; U-100% 15N]1
150 mMMAGNESIUM Chloride-21
20 mMMES-31
200 mMsodium chloride-41
5 mMcalcium chloride-51
10 mMDTT-61
50 uMDSS-71
0.02 %sodium azide-81
90 %H2O-91
10 %D2O-101
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichrefinement,geometry optimization,structure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis,peak picking,chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
CARAKeller and Wuthrichchemical shift assignment
MOLMOLKoradi, Billeter and Wuthrichrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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