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- PDB-2kq2: Solution NMR structure of the apo form of a ribonuclease H domain... -

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Basic information

Entry
Database: PDB / ID: 2kq2
TitleSolution NMR structure of the apo form of a ribonuclease H domain of protein DSY1790 from Desulfitobacterium hafniense, Northeast Structural Genomics target DhR1A
ComponentsRibonuclease H-related protein
KeywordsHYDROLASE / PSI / NESG / protein structure / Ribonuclease H / apo enzyme / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
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
Ribonuclease H-related protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense DCB-2 (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, 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: Solution NMR structure of the apo form of a ribonuclease H domain of protein DSY1790 from Desulfitobacterium hafniense, Northeast Structural Genomics 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
DepositionOct 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H-related protein


Theoretical massNumber of molelcules
Total (without water)16,6931
Polymers16,6931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribonuclease H-related protein


Mass: 16692.633 Da / Num. of mol.: 1 / Fragment: sequence database residues 69-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria)
Strain: DCB-2 / DSM 10664 / Gene: Dhaf_2944 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: B8FYP4

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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
1322D 1H-13C HSQC
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-COSY
1913D simultaneous NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.89 mM [U-99% 13C; U-99% 15N] DhR1A, 10 v/v [U-2H] D2O, 90 v/v H2O, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.943 mM [U-5% 13C; U-99% 15N] DhR1A, 10 v/v [U-2H] D2O, 90 v/v H2O, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 w/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.89 mMDhR1A-1[U-99% 13C; U-99% 15N]1
10 v/vD2O-2[U-2H]1
90 v/vH2O-31
20 mMMES-41
200 mMsodium chloride-51
5 mMcalcium chloride-61
10 mMDTT-71
50 uMDSS-81
0.02 w/vsodium azide-91
0.943 mMDhR1A-10[U-5% 13C; U-99% 15N]2
10 v/vD2O-11[U-2H]2
90 v/vH2O-122
20 mMMES-132
200 mMsodium chloride-142
5 mMcalcium chloride-152
10 mMDTT-162
50 uMDSS-172
0.02 w/vsodium azide-182
Sample conditionsIonic strength: 430 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityPlusVarianUNITYPLUS6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
SPSCANGlaserprocessing
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CSIWishart and Sykesstructure solution
TALOSCornilescu, Delaglio and Baxstructure solution
CYANAHerrmann, Guntert and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
MOLMOLKoradi, Billeter and Wuthrichrefinement
PSVSBhattacharya and Montelionerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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