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- PDB-2kz6: Solution structure of protein CV0426 from Chromobacterium violace... -

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Basic information

Entry
Database: PDB / ID: 2kz6
TitleSolution structure of protein CV0426 from Chromobacterium violaceum, Northeast structural genomics consortium (NESG) target CVT2
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein of unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHelix Hairpins - #1310 / Phage tail assembly chaperone protein / Phage tail assembly chaperone protein / Helix Hairpins / Helix non-globular / Special / Uncharacterized protein
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsLemak, A. / Yee, A. / Lee, H. / Semesi, A. / Prestegard, J. / Montelione, G.T. / Arrowsmith, C. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution structure of protein CV0426 from Chromobacterium violaceum
Authors: Lemak, A. / Yee, A. / Lee, H. / Semesi, A. / Prestegard, J. / Montelione, G.T. / Arrowsmith, C.
History
DepositionJun 11, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / 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_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _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

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)11,6121
Polymers11,6121
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 11612.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: CV_0426 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7P0Y9
Sequence detailsTHE SEQUENCE PROVIDED IS THE TRANSLATED PLASMID SEQUENCE OBTAINED FROM CHROMOBACTERIUM VIOLACEUM ...THE SEQUENCE PROVIDED IS THE TRANSLATED PLASMID SEQUENCE OBTAINED FROM CHROMOBACTERIUM VIOLACEUM ATCC 12472 GENOMIC DNA CLONING. THE SEQUENCE OF THE PROTEIN THAT WAS SOLVED HAS GLUTAMIC ACID IN RESIDUE 7 AND NOT GLUTAMINE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D 1H-13C arom NOESY
11012D 1H-15N HSQC (IPAP)

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] cv0426-1, 10 mM MOPS-2, 450 mM sodium chloride-3, 10 uM ZnSO4-4, 10 mM DTT-5, 0.01 % NaN3-6, 10 mM benzamidine-7, 10 % D2O-8, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMcv0426-1[U-13C; U-15N]1
10 mMMOPS-21
450 mMsodium chloride-31
10 uMZnSO4-41
10 mMDTT-51
0.01 %NaN3-61
10 mMbenzamidine-71
10 %D2O-81
Sample conditionsIonic strength: 450 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak, Steren, Llinas, Arrowsmithchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1 / Details: refinment in water bath with RDC restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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