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- PDB-6y8v: Rhodospirillum rubrum oxidized CooT solution structure -

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Basic information

Entry
Database: PDB / ID: 6y8v
TitleRhodospirillum rubrum oxidized 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 oxidized 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 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 area1890 Å2
ΔGint-11 kcal/mol
Surface area8460 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
Has protein modificationY

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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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
1141isotropic13D (H)CCH-TOCSY
1131isotropic13D HNCA
1121isotropic13D H(CCO)NH
1111isotropic13D HNCO
1101isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] CooT, 90% H2O/10% D2O, 1 mM EDTA
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: CooT / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6 / 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
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1
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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