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- PDB-1mjg: CRYSTAL STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mjg | ||||||
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Title | CRYSTAL STRUCTURE OF BIFUNCTIONAL CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE(CODH/ACS) FROM MOORELLA THERMOACETICA (F. CLOSTRIDIUM THERMOACETICUM) | ||||||
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![]() | OXIDOREDUCTASE / Carbon monoxide dehydrogenase(CODH) / Acetyl-CoA Synthase (ACS) / Nickel-Iron-Sulfur cluster (Ni-Fe-S) / Nickel-Coopper-Iron-Sulfur (Ni-Cu-Fe-S) Cluster / Hydrophobic CO channel / substrate tunnel / Helical domain / Rossmann fold / Electron transfer / Clostridium thermoaceticum / Wood-Ljundahl pathway | ||||||
Function / homology | ![]() CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / carbon fixation / nickel cation binding / generation of precursor metabolites and energy ...CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon monoxide dehydrogenase / anaerobic carbon-monoxide dehydrogenase activity / : / acetyl-CoA metabolic process / hydroxylamine reductase activity / carbon fixation / nickel cation binding / generation of precursor metabolites and energy / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Doukov, T.I. / Iverson, T.M. / Seravalli, J. / Ragsdale, S.W. / Drennan, C.L. | ||||||
![]() | ![]() Title: A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase Authors: Doukov, T.I. / Iverson, T.M. / Seravalli, J. / Ragsdale, S.W. / Drennan, C.L. | ||||||
History |
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Remark 600 | HETEROGEN The A-Cluster consists of FS4 900, CU 901 and NI 902 for chains M,N,O,P. There is ...HETEROGEN The A-Cluster consists of FS4 900, CU 901 and NI 902 for chains M,N,O,P. There is electron density for a ligand on the Cu of the A-cluster. An acetyl moiety (ACT) has been refined in this position, although the exact nature of this ligand is unknown. | ||||||
Remark 999 | SEQUENCE Position 685 of the ACS subunit (chains M,N,O,P) has been modeled as Ser according to the ...SEQUENCE Position 685 of the ACS subunit (chains M,N,O,P) has been modeled as Ser according to the PIR B41670 sequence entry. The Swissprot P27988 entry lists position 685 as Arg. The electron density can be interpreted as Arg or as Ser hydrogen bonded to water molecules. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 901.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jqkS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules ABCDMNOP
#1: Protein | Mass: 73006.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P27989, carbon-monoxide dehydrogenase (acceptor) #2: Protein | Mass: 81746.812 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P27988, carbon-monoxide dehydrogenase (acceptor) |
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-Non-polymers , 6 types, 1255 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/XCC.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/XCC.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-XCC / #5: Chemical | ChemComp-CU1 / #6: Chemical | ChemComp-NI / #7: Chemical | ChemComp-ACT / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 8 % PEG monomethyl ether 5000, 20% Glycerol, 200 mM Calcium Acetate, 100 mM PIPES pH 6.5, 2 mM dithioerythritol, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 332287 / Num. obs: 313013 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.3 % / Biso Wilson estimate: 30.4 Å2 / Rsym value: 0.093 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.28 Å / Rsym value: 0.39 / % possible all: 91.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 1031478 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 91.3 % / Rmerge(I) obs: 0.39 |
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Processing
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Refinement | Method to determine structure: ![]() ![]() Starting model: PDB ENTRY 1JQK Resolution: 2.2→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Disordered regions include residues 1-2 and 536-540 of the CODH subunits (chains A-D) and residues 1, 313-320 of the ACS subunits (chains M-P). Also, the second and third domains of ACS ...Details: Disordered regions include residues 1-2 and 536-540 of the CODH subunits (chains A-D) and residues 1, 313-320 of the ACS subunits (chains M-P). Also, the second and third domains of ACS subunit chain O have poor electron density and high B factors compared to the other ACS subunits.
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Solvent computation | Solvent model: CNS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.252 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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