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- PDB-3kjg: ADP-bound state of CooC1 -

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Basic information

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


ATP binding / metal ion binding
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,8484
Polymers55,9932
Non-polymers8542
Water4,089227
1
A: CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4242
Polymers27,9971
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
hetero molecules

B: CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8484
Polymers55,9932
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.690, 241.190, 72.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-277-

HOH

21B-318-

HOH

DetailsBiological oligomeric state is monomer and dimer equilibrium

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Components

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


Mass: 27996.701 Da / Num. of mol.: 2 / Fragment: CooC1 ATPase
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: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.2 M lithium citrate tribasic, 14% PEG3350, 5% Glycerol, 1 mM ADP, pH 8.4, 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: Mar 11, 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: 29710 / % possible obs: 99.5 % / Observed criterion σ(F): 2
Reflection shellResolution: 2.3→2.4 Å / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.64 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.274 1486 5 %
Rwork0.232 --
obs-29710 99.5 %
Solvent computationBsol: 45.289 Å2
Displacement parametersBiso max: 157.37 Å2 / Biso mean: 49.622 Å2 / Biso min: 15.25 Å2
Baniso -1Baniso -2Baniso -3
1-8.606 Å20 Å20 Å2
2---6.466 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 54 227 4199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.497
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4PRODRG-ADP.par

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