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- PDB-5n76: Crystal structure of the apo-form of the CO dehydrogenase accesso... -

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Basic information

Entry
Database: PDB / ID: 5n76
TitleCrystal structure of the apo-form of the CO dehydrogenase accessory protein CooT from Rhodospirillum rubrum
ComponentsCooT
Keywordsnickel-binding protein / CODH maturation / anaerobic metabolism
Function / homologyCO dehydrogenase accessory protein CooT / CO dehydrogenase accessory protein CooT / CooT
Function and homology information
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsTimm, J. / Brochier-Armanet, C. / Perard, J. / Zambelli, B. / Ollagnier-de-Choudens, S. / Ciurli, S. / Cavazza, C.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation Simone Del DucaCAJ-14-166 France
CitationJournal: Metallomics / Year: 2017
Title: The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein.
Authors: Timm, J. / Brochier-Armanet, C. / Perard, J. / Zambelli, B. / Ollagnier-de-Choudens, S. / Ciurli, S. / Cavazza, C.
History
DepositionFeb 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Oct 23, 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

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Assembly

Deposited unit
A: CooT
D: CooT
B: CooT
C: CooT
E: CooT
F: CooT


Theoretical massNumber of molelcules
Total (without water)42,6316
Polymers42,6316
Non-polymers00
Water4,306239
1
A: CooT
D: CooT


Theoretical massNumber of molelcules
Total (without water)14,2102
Polymers14,2102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area7160 Å2
MethodPISA
2
B: CooT
C: CooT


Theoretical massNumber of molelcules
Total (without water)14,2102
Polymers14,2102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-10 kcal/mol
Surface area7280 Å2
MethodPISA
3
E: CooT
F: CooT


Theoretical massNumber of molelcules
Total (without water)14,2102
Polymers14,2102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-11 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.943, 108.943, 110.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
CooT


Mass: 7105.162 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: MCMAKVVLTKADGGRVEIGDVLEVRAEGGAVRVTTLFDEEHAFPGLAIGRVDLRSGVISL IEEQNR
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: cooT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P72320
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50 mM sodium acetate pH 4.6, 100 mM CaCl2 and 16% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→44.59 Å / Num. obs: 52618 / % possible obs: 99.2 % / Redundancy: 7.26 % / Net I/σ(I): 10.84

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→44.59 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs49987 99.2 %
Refinement stepCycle: LAST / Resolution: 1.9→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 0 239 2987

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