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Yorodumi- PDB-1cc1: CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cc1 | ||||||
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Title | CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NI-FE-SE HYDROGENASE | ||||||
Function / homology | Function and homology information hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfomicrobium baculatum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Garcin, E. / Vernede, X. / Hatchikian, E.C. / Volbeda, A. / Frey, M. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center Authors: Garcin, E. / Vernede, X. / Hatchikian, E.C. / Volbeda, A. / Frey, M. / Fontecilla-Camps, J.C. #1: Journal: J.Am.Chem.Soc. / Year: 1996 Title: Structure of the [NiFe] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands Authors: Volbeda, A. / Garcin, E. / Piras, C. / De Lacey, A.L. / Fernandez, V.M. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cc1.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cc1.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cc1_validation.pdf.gz | 414.8 KB | Display | wwPDB validaton report |
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Full document | 1cc1_full_validation.pdf.gz | 423 KB | Display | |
Data in XML | 1cc1_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1cc1_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/1cc1 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/1cc1 | HTTPS FTP |
-Related structure data
Related structure data | 2frvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules SL
#1: Protein | Mass: 30888.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfomicrobium baculatum (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P13063, 1.18.99.1 |
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#2: Protein | Mass: 55217.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COMPLEXED WITH IRON/SULFUR CLUSTER, CARBONMONOXIDE-(DICYANO) IRON, HYDROSULFURIC ACID Source: (natural) Desulfomicrobium baculatum (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P13065, 1.18.99.1 |
-Non-polymers , 6 types, 326 molecules
#3: Chemical | #4: Chemical | ChemComp-NI / | #5: Chemical | ChemComp-FE2 / | #6: Chemical | ChemComp-FCO / | #7: Chemical | ChemComp-H2S / | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | IRON(II) WITH 1 CARBON MONOXIDE AND 2 CYANIDE LIGANDS. |
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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 Å3/Da / Density % sol: 38.4 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.98 |
Detector | Detector: CCD / Date: Oct 1, 1996 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 36050 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.083 |
Reflection shell | Resolution: 2.15→2.18 Å / Rsym value: 0.202 / % possible all: 48.8 |
Reflection | *PLUS Num. measured all: 201153 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 48.8 % / Rmerge(I) obs: 0.202 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FRV Resolution: 2.15→8 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.857 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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