+Open data
-Basic information
Entry | Database: PDB / ID: 1ffv | ||||||
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Title | CARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA | ||||||
Components |
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Keywords | HYDROLASE / DEHYDROGENASE | ||||||
Function / homology | Function and homology information aerobic carbon monoxide dehydrogenase / carbon-monoxide oxygenase activity / : / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / iron ion binding / copper ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Hydrogenophaga pseudoflava (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Haenzelmann, P. / Dobbek, H. / Gremer, L. / Huber, R. / Meyer, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase. Authors: Hanzelmann, P. / Dobbek, H. / Gremer, L. / Huber, R. / Meyer, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ffv.cif.gz | 510.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ffv.ent.gz | 411.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ffv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ffv_validation.pdf.gz | 714.2 KB | Display | wwPDB validaton report |
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Full document | 1ffv_full_validation.pdf.gz | 759.7 KB | Display | |
Data in XML | 1ffv_validation.xml.gz | 52.8 KB | Display | |
Data in CIF | 1ffv_validation.cif.gz | 87.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1ffv ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1ffv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 17747.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: UniProt: P19915 #2: Protein | Mass: 87345.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: GenBank: 4098682, UniProt: P19913*PLUS #3: Protein | Mass: 30552.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hydrogenophaga pseudoflava (bacteria) / References: UniProt: P19914 |
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-Non-polymers , 4 types, 1615 molecules
#4: Chemical | ChemComp-FES / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 3.37 Å3/Da / Density % sol: 63.53 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: potassium sodium tartrate, dihydrogen ammonium phosphate, methylpentandediol, dithioerythritol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 K | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 433970 / Num. obs: 407833 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.25→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.358 / Num. unique all: 165339 / % possible all: 79.7 |
Reflection | *PLUS Num. obs: 162740 / Num. measured all: 433970 |
Reflection shell | *PLUS % possible obs: 79.7 % |
-Processing
Software |
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Refinement | Resolution: 2.25→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.209 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 2.32 Å / Rfactor Rfree: 0.341 / Rfactor obs: 0.323 |