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Yorodumi- PDB-1jqk: Crystal structure of carbon monoxide dehydrogenase from Rhodospir... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jqk | ||||||
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Title | Crystal structure of carbon monoxide dehydrogenase from Rhodospirillum rubrum | ||||||
Components | carbon monoxide dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / generation of precursor metabolites and energy / ferrous iron binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / protein homodimerization activity ...anaerobic carbon monoxide dehydrogenase / carbon-monoxide dehydrogenase (ferredoxin) activity / carbon-monoxide dehydrogenase (acceptor) activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / generation of precursor metabolites and energy / ferrous iron binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / protein homodimerization activity / protein-containing complex / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rhodospirillum rubrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Drennan, C.L. / Heo, J. / Sintchak, M.D. / Schreiter, E. / Ludden, P.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase. Authors: Drennan, C.L. / Heo, J. / Sintchak, M.D. / Schreiter, E. / Ludden, P.W. | ||||||
History |
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Remark 600 | HETEROGEN The ligand WCC is a Ni-Fe-S cubane. There is an unidentified ligand, UNX, bound to the Ni ...HETEROGEN The ligand WCC is a Ni-Fe-S cubane. There is an unidentified ligand, UNX, bound to the Ni of the WCC. There is also a FE2 bound to the cubane. The C-cluster, as it is called, has a single iron site (FE2) and a four-metal cubane (Ni-Fe-S). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jqk.cif.gz | 655.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jqk.ent.gz | 540.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/1jqk ftp://data.pdbj.org/pub/pdb/validation_reports/jq/1jqk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The homodimer is the biological unit. |
-Components
#1: Protein | Mass: 66927.969 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: COOS gene / Source: (natural) Rhodospirillum rubrum (bacteria) References: UniProt: P31896, carbon-monoxide dehydrogenase (acceptor) #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-WCC / #5: Chemical | ChemComp-UNX / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.92 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: capillary crystallization / pH: 7.5 Details: 10% PEG 8000, 0.1 M Tris buffer, 0.4 M calcium chloride, 5% 2-methyl-2,4-pentanediol, pH 7.5, capillary crystallization, temperature 298.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.3 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jul 30, 2000 / Details: condensing mirror |
Radiation | Monochromator: two crystal non-dispersive monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 90759 / % possible obs: 94 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 2.5 % / Biso Wilson estimate: 63.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 7792 / Rsym value: 0.356 / % possible all: 80.8 |
Reflection | *PLUS Num. measured all: 223988 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 80.1 % / Rmerge(I) obs: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→100 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: bulk solvent correction, NCS restraints, maximum likelihood target, cartesian molecular dynamics. There are 3 homodimers in the asymmetric unit: chains A&B, C&D, and E&F. Molecules C&D, E&F ...Details: bulk solvent correction, NCS restraints, maximum likelihood target, cartesian molecular dynamics. There are 3 homodimers in the asymmetric unit: chains A&B, C&D, and E&F. Molecules C&D, E&F have lower B-factors than A&B, and are the molecules that should be considered in structural analyses. No side chain density was seen for residue 348.
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Displacement parameters | Biso mean: 47.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→100 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 100 Å / σ(F): 2 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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