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- PDB-1nxi: Solution structure of Vibrio cholerae protein VC0424 -

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Basic information

Entry
Database: PDB / ID: 1nxi
TitleSolution structure of Vibrio cholerae protein VC0424
Componentsconserved hypothetical protein VC0424
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ab sandwich / COG 3076 / ATCC no. 51394D / NESG TARGET OP3 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


endoribonuclease inhibitor activity / enzyme binding / cytoplasm
Similarity search - Function
RraB-like / Regulator of ribonuclease activity B domain / Regulator of ribonuclease activity B / RraB-like superfamily / Regulator of ribonuclease activity B / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulator of ribonuclease activity B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsRamelot, T.A. / Ni, S. / Goldsmith-Fischman, S. / Cort, J.R. / Honig, B. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Protein Sci. / Year: 2003
Title: Solution structure of Vibrio cholerae protein VC0424: a variation of the ferredoxin-like fold.
Authors: Ramelot, T.A. / Ni, S. / Goldsmith-Fischman, S. / Cort, J.R. / Honig, B. / Kennedy, M.A.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _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: conserved hypothetical protein VC0424


Theoretical massNumber of molelcules
Total (without water)15,3421
Polymers15,3421
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 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein conserved hypothetical protein VC0424


Mass: 15341.780 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC0424 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (lamdaDE3) / References: UniProt: Q9KUU1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
2414D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM VC0424_delta16c, U-15N, 13C, Tris, pH 7.290% H2O/10% D2O
21.5mM VC0424_delta16c, U-15N, 13C, Tris, pH 6.899% H2O, 1% D2O
Sample conditionsIonic strength: 20mM Tris HCl, 500mM NaCl / pH: 7.8 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003
Varian UNITYVarianUNITY6004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH-2.0.4Schwieters, Kuszewski, Tjandra, Clorestructure solution
Felix98MSIprocessing
VNMR6.1CVariancollection
Sparky3.98Goddard, Knellerdata analysis
X-PLORNIH-2.0.4Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1263 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 1030; INTRA-RESIDUE [I=J] = 5; SEQUENTIAL [(I-J)=1] = 250; MEDIUM ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1263 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 1030; INTRA-RESIDUE [I=J] = 5; SEQUENTIAL [(I-J)=1] = 250; MEDIUM RANGE [1<(I-J)<5] = 329; LONG RANGE [(I-J)>=5] = 446; HYDROGEN BOND CONSTRAINTS = 116 (2 PER H-BOND); NUMBER OF DISTANCE CONSTRAINTS PER RESIDUE = 9.0; DIHEDRAL-ANGLE CONSTRAINTS = 117 (44 PHI, 62 PSI, 11 CHI1); TOTAL NUMBER OF CONSTRAINTS PER RESIDUE = 11.0 (RESIDES 9-124); NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 3.9; NUMBER OF STRUCTURES COMPUTED = 20; NUMBER OF STRUCTURES USED = 20. AVERAGE DISTANCE VIOLATIONS >0.001 ANG = 27.7; AVERAGE R.M.S. DISTANCE VIOLATION = 0.002 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 36. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.001 DEG = 2.0; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 4 DEG; AVERAGE R.M.S. ANGLE VIOLATION = 0.03 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C',O) = 0.51 ANG; ALL HEAVY ATOMS = 1.03 ANG; PROCHECK: MOST FAVORED REGIONS = 82%; ADDITIONAL ALLOWED REGIONS = 16%; GENEROUSLY ALLOWED REGIONS = 1%; DISALLOWED REGIONS = 1%.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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