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- PDB-2kks: Solution Structure Of Protein DSY2949 From Desulfitobacterium haf... -

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Basic information

Entry
Database: PDB / ID: 2kks
TitleSolution Structure Of Protein DSY2949 From Desulfitobacterium hafniense. Northeast Structural Genomics Consortium Target DhR27
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


: / metallopeptidase activity
Similarity search - Function
JAB domain, prokaryotic / Prokaryotic homologs of the JAB domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MPN domain-containing protein
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, Y. / Mills, J.L. / Wang, H. / Ciccosanti, C. / Jiang, M. / Sukumaran, D. / Zhang, Q. / Nair, R. / Rost, B. / Acton, T. ...Wu, Y. / Mills, J.L. / Wang, H. / Ciccosanti, C. / Jiang, M. / Sukumaran, D. / Zhang, Q. / Nair, R. / Rost, B. / Acton, T. / Xiao, R. / Swapna, G.V.T. / Everett, J. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure Of Protein DSY2949 From Desulfitobacterium hafniense. Northeast Structural Genomics Consortium Target DhR27
Authors: Wu, Y. / Mills, J.L. / Wang, H. / Ciccosanti, C. / Jiang, M. / Sukumaran, D. / Zhang, Q. / Nair, R. / Rost, B. / Acton, T. / Xiao, R. / Swapna, G.V.T. / Everett, J. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 7, 2012Group: Database references / Structure summary
Revision 1.3Feb 26, 2020Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,8231
Polymers16,8231
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 16823.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: Y51 / Gene: DSY2949 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q24TA4

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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-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D (H)CCH-TOCSY
171simNOESY
1813D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-10% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMprotein-1[U-100% 13C; U-100% 15N]1
0.9 mMprotein-2[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.2 / pH: 4.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionerefinement
TALOSCornilescu, Delaglio and Baxrefinement
XEASYBartels et al.chemical shift assignment
RefinementMethod: simulated annealing / 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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