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- PDB-2x8n: Solution NMR structure of uncharacterized protein CV0863 from Chr... -

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Basic information

Entry
Database: PDB / ID: 2x8n
TitleSolution NMR structure of uncharacterized protein CV0863 from Chromobacterium violaceum. NORTHEAST STRUCTURAL GENOMICS TARGET (NESG) target CvT3. OCSP target CV0863.
ComponentsCV0863
KeywordsSTRUCTURAL GENOMICS / NON-UNIFORM SAMPLING / MULTIDIMENSIONAL DECOMPOSITION / ABACUS / FRAGMENT MONTE CARLO / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / ONTARIO CENTRE FOR STRUCTURAL PROTEOMICS / OCSP
Function / homologyUncharacterised protein PF10387, DUF2442 / Protein of unknown function DUF2442 / Protein of unknown function (DUF2442) / NE0471 N-terminal domain-like / 2-Layer Sandwich / Alpha Beta / DUF2442 domain-containing protein
Function and homology information
Biological speciesCHROMOBACTERIUM VIOLACEUM ATCC 12472 (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, RESTRAINED MOLECULAR DYNAMICS
AuthorsGutmanas, A. / Fares, C. / Yee, A. / Lemak, A. / Semesi, A. / Arrowsmith, C.H. / Ontario Centre for Structural Proteomics (OCSP) / Northeast Structural Genomics Consortium (NESG)
Citation
Journal: To be Published
Title: Solution NMR Structure of Uncharacterized Protein Cv0863 from Chromobacterium Violaceum
Authors: Gutmanas, A. / Fares, C. / Yee, A. / Lemak, A. / Arrowsmith, C.H.
#1: Journal: J.Biomol.NMR / Year: 2011
Title: A Novel Strategy for NMR Resonance Assignment and Protein Structure Determination.
Authors: Lemak, A. / Gutmanas, A. / Chitayat, S. / Karra, M. / Fares, C. / Sunnerhagen, M. / Arrowsmith, C.H.
History
DepositionMar 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Atomic model / Database references / Version format compliance
Revision 1.2May 6, 2015Group: Derived calculations / Structure summary
Revision 1.3Jan 17, 2018Group: Data collection / Category: pdbx_nmr_spectrometer
Item: _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.4Jan 15, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 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 1.6Jun 19, 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: CV0863


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein CV0863


Mass: 12507.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHROMOBACTERIUM VIOLACEUM ATCC 12472 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q7NZQ8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-NOESY-HSQC-ALIPHATIC
12113C-HSQC-CT-ALIPHATIC
13113C-HSQC-ALIPHATIC
14113C-HSQC-AROMATIC
15115N-HSQ
16113C-NOESY-HSQC-AROMATIC
17115N-NOESY-HSQC
181H(C)CH-TOCSY- ALIPHATIC
191(H)CCH-TOCSY- ALIPHATIC
1101H(C)CH-TOCSY-AROMATIC
1111(H)CCH-TOCSY-AROMATIC
1121T1
1131T1RHO
1141HNCO
1151HNCA
1161CBCA(CO)NH
1171HBHA(CBCACO)NH
1181H(CCCO)NH-TOCSY
119113C-HSQC-CT-ALIPHATIC
NMR detailsText: ALL 3D NMR SPECTRA WERE COLLECTED WITH NON-UNIFORM SAMPLING (WWW.NMR2.BUFFALO.EDU/NESG.WIKI/SETTING_UP_NON- UNIFORMLY_SAMPLED_SPECTRA) AND PROCESSED WITH MDDGUI AND MDDNMR SOFTWARE (WWW.NMR2. ...Text: ALL 3D NMR SPECTRA WERE COLLECTED WITH NON-UNIFORM SAMPLING (WWW.NMR2.BUFFALO.EDU/NESG.WIKI/SETTING_UP_NON- UNIFORMLY_SAMPLED_SPECTRA) AND PROCESSED WITH MDDGUI AND MDDNMR SOFTWARE (WWW.NMR2.BUFFALO.EDU/NESG.WIKI/ PROCESSING_ NON-UNIFORMLY_SAMPLED_SPECTRA_WITH_MULTIDIMENSIONAL_ DECOMPOSITION

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Sample preparation

Details
Solution-IDContents
190% H2O/10% D2O, 10MM TRIS,300 MM NACL,10 MM ZNSO4,10 MM DTT, 1 MM BENZAMIDINE,0.01% NAN3,1X ROCHE INHIBITOR COCKTAIL, 100% 13C, 100% 15N-CV0863 1MM
290% H2O/10% D2O, 10MM TRIS,300 MM NACL,10 MM ZNSO4,10 MM DTT, 1 MM BENZAMIDINE,0.01% NAN3,1X ROCHE INHIBITOR COCKTAIL, 7% 13C, 100% 15N-CV0863 1MM
Sample conditionsIonic strength: 300 mM / pH: 7 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER, ADAMS,CLORE,GROS,NILGES,READrefinement
NMRPipestructure solution
MddNMRstructure solution
MDDGUIstructure solution
ABACUSstructure solution
CcpNmr AnalysisANAYSISstructure solution
CYANAstructure solution
CNSstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS, RESTRAINED MOLECULAR DYNAMICS
Software ordinal: 1 / Details: RESTRAINED MOLECULAR DYNAMICS
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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