[English] 日本語
Yorodumi- PDB-1oao: NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha sub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oao | ||||||
---|---|---|---|---|---|---|---|
Title | NiZn[Fe4S4] and NiNi[Fe4S4] clusters in closed and open alpha subunits of acetyl-CoA synthase/carbon monoxide dehydrogenase | ||||||
Components | (CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE/TRANSFERASE / OXIDOREDUCTASE-TRANSFERASE COMPLEX / ELECTRON TRANSFER / OXIDOREDUCTASE / ACETYL-COA FORMATION / WOOD/LJUNGDAHL PATHWAY / NICKEL | ||||||
Function / homology | Function and homology information 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 | MOORELLA THERMOACETICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, MAD / Resolution: 1.9 Å | ||||||
Authors | Darnault, C. / Volbeda, A. / Kim, E.J. / Legrand, P. / Vernede, X. / Lindahl, P.A. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Ni-Zn-[Fe4-S4] and Ni-Ni-[Fe4-S4] Clusters in Closed and Open Alpha Subunits of Acetyl-Coa Synthase/Carbon Monoxide Dehydrogenase Authors: Darnault, C. / Volbeda, A. / Kim, E.J. / Legrand, P. / Vernede, X. / Lindahl, P.A. / Fontecilla-Camps, J.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1oao.cif.gz | 573.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1oao.ent.gz | 467.3 KB | Display | PDB format |
PDBx/mmJSON format | 1oao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oao_validation.pdf.gz | 571.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1oao_full_validation.pdf.gz | 631.7 KB | Display | |
Data in XML | 1oao_validation.xml.gz | 111.9 KB | Display | |
Data in CIF | 1oao_validation.cif.gz | 161 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oao ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oao | HTTPS FTP |
-Related structure data
Related structure data | 1jjy S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.161329, -0.978881, -0.125561), Vector: |
-Components
-CARBON MONOXIDE DEHYDROGENASE/ACETYL-COA SYNTHASE SUBUNIT ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 73006.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MOORELLA THERMOACETICA (bacteria) References: UniProt: P27989, carbon-monoxide dehydrogenase (acceptor), anaerobic carbon monoxide dehydrogenase #2: Protein | Mass: 81816.930 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MOORELLA THERMOACETICA (bacteria) References: UniProt: P27988, CO-methylating acetyl-CoA synthase |
---|
-Non-polymers , 12 types, 1328 molecules
#3: Chemical | ChemComp-SF4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-GOL / #8: Chemical | #9: Chemical | ChemComp-BCT / | #10: Chemical | ChemComp-ZN / | #11: Chemical | #12: Chemical | ChemComp-SX / | #13: Chemical | ChemComp-ACT / | #14: Water | ChemComp-HOH / | |
---|
-Details
Compound details | CATALYZES THE INTERCONVERSION OF CO AND CO2 AND THE SYNTHESIS OF ACETYL-COENZYME A FROM THE ...CATALYZES THE INTERCONVE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.2 / Details: pH 7.20 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.2 Å / Num. obs: 479707 / % possible obs: 94.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.238 / % possible all: 67.9 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Num. obs: 239946 |
Reflection shell | *PLUS % possible obs: 67.9 % / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT, MAD Starting model: PDB ENTRY 1JJY 1jjy Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.296 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.79 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|