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- PDB-3kji: Zn and ADP bound state of CooC1 -

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Basic information

Entry
Database: PDB / ID: 3kji
TitleZn and ADP bound state of CooC1
ComponentsCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
KeywordsHYDROLASE / METAL BINDING PROTEIN / Zn/ADP-bound dimer / 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
ADENOSINE-5'-DIPHOSPHATE / CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 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 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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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)56,9796
Polymers55,9932
Non-polymers9854
Water8,125451
1
A: CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,9796
Polymers55,9932
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
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)56,9796
Polymers55,9932
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)114.353, 81.760, 86.578
Angle α, β, γ (deg.)90.000, 128.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-255-

ZN

21B-255-

ZN

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Components

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


Mass: 27996.701 Da / Num. of mol.: 2
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 0.2 M Lithium citrate tribasic, 10% PEG3350, 5% Glycerol, 10 mM AlF4, 10 mM MgCl2, 1 mM ADP, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MX-225 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 34673 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3
Reflection shellResolution: 2.13→2.19 Å / % possible all: 99.9

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→19.69 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.278 1734 5 %
Rwork0.224 --
obs-34672 99.6 %
Solvent computationBsol: 44.447 Å2
Displacement parametersBiso max: 160.47 Å2 / Biso mean: 50.814 Å2 / Biso min: 15.74 Å2
Baniso -1Baniso -2Baniso -3
1-7.077 Å20 Å26.41 Å2
2--4.074 Å20 Å2
3----11.151 Å2
Refinement stepCycle: LAST / Resolution: 2.13→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3918 0 56 451 4425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.489
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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