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- PDB-6y8w: Rhodospirillum rubrum reduced CooT solution structure -

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Basic information

Entry
Database: PDB / ID: 6y8w
TitleRhodospirillum rubrum reduced CooT solution structure
ComponentsCooT
KeywordsMETAL BINDING PROTEIN / NICKEL-BINDING PROTEIN / ANAEROBIC METABOLISM
Function / homologyCO dehydrogenase accessory protein CooT / CO dehydrogenase accessory protein CooT / CooT
Function and homology information
Biological speciesRhodospirillum rubrum (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsChagot, B.
CitationJournal: To Be Published
Title: Rhodospirillum rubrum reduced CooT solution structure
Authors: Chagot, B.
History
DepositionMar 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 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: CooT
B: CooT


Theoretical massNumber of molelcules
Total (without water)14,8072
Polymers14,8072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1910 Å2
ΔGint-9 kcal/mol
Surface area8620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein CooT


Mass: 7403.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: cooT / Production host: Escherichia coli (E. coli) / References: UniProt: P72320

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D (H)CCH-TOCSY
171isotropic13D C(CO)NH
161isotropic13D 1H-15N NOESY
181isotropic13D 1H-15N NOESY
1111isotropic12D 1H-13C HSQC aliphatic
1101isotropic12D 1H-13C HSQC aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] CooT, 90% H2O/10% D2O, 5 mM EDTA, 0.5 mM TCEP
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: CooT / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0.1 M / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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