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- PDB-3kje: Empty state of CooC1 -

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Basic information

Entry
Database: PDB / ID: 3kje
TitleEmpty state of CooC1
ComponentsCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
KeywordsHYDROLASE / METAL BINDING PROTEIN / nickel binding protein / ATPase
Function / homology
Function and homology information


negative regulation of cell division / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Nickel insertion ATPase/GTPase (CO dehydrogenase maturation factor), CooC type / CobQ/CobB/MinD/ParA nucleotide binding domain / CobQ/CobB/MinD/ParA nucleotide binding domain / : / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJeoung, J.-H. / Dobbek, H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of the ATP-Dependent Maturation Factor of Ni,Fe-Containing Carbon Monoxide Dehydrogenases
Authors: Jeoung, J.H. / Giese, T. / Grunwald, M. / Dobbek, H.
History
DepositionNov 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC


Theoretical massNumber of molelcules
Total (without water)27,9971
Polymers27,9971
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.110, 80.110, 76.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC


Mass: 27996.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (bacteria)
Strain: Z-2901 / Gene: CHY_1220, cooC1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3ACS5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG3350, 0.1 M HEPES-NaOH pH7.5, 0.2M L-proline, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2008 / Details: osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12969 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Net I/σ(I): 34.65
Reflection shellResolution: 2.3→2.4 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.38 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2826 649 RANDOM
Rwork0.2311 --
all-13052 -
obs-12969 -
Refinement stepCycle: LAST / Resolution: 2.3→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 0 143 2102

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