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Yorodumi- PDB-1fwx: CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fwx | ||||||
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Title | CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS | ||||||
Components | NITROUS OXIDE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / Beta-propeller domain / cupredoxin domain / CuZ site / CuA site | ||||||
Function / homology | Function and homology information nitrous-oxide reductase / nitrous-oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / periplasmic space / copper ion binding / calcium ion binding / membrane Similarity search - Function | ||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Brown, K. / Djinovic-Carugo, K. / Haltia, T. / Cabrito, I. / Saraste, M. / Moura, J.J. / Moura, I. / Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Revisiting the Catalytic CuZ Cluster of Nitrous Oxide (N2O) Reductase. Evidence of a Bridging Inorganic Sulfur Authors: Brown, K. / Djinovic-Carugo, K. / Haltia, T. / Cabrito, I. / Saraste, M. / Moura, J.J. / Moura, I. / Tegoni, M. / Cambillau, C. #1: Journal: BIOCHEM.J. / Year: 2003 Title: Crystal structure of nitrous oxide reductase from Paracoccus denitrificans at 1.6 A resolution Authors: Haltia, T. / Brown, K. / Tegoni, M. / Cambillau, C. / Saraste, M. / Mattila, K. / Djinovic-Carugo, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fwx.cif.gz | 530.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fwx.ent.gz | 424 KB | Display | PDB format |
PDBx/mmJSON format | 1fwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/1fwx ftp://data.pdbj.org/pub/pdb/validation_reports/fw/1fwx | HTTPS FTP |
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-Related structure data
Related structure data | 1qniS 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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2 |
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Unit cell |
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Details | The biological assembly is a dimer constructed from chains A and B, and C and D, related by the non-crystallographic two-fold. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 66397.500 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: Q51705, EC: 1.7.99.6 |
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-Non-polymers , 5 types, 2665 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CUA / #5: Chemical | ChemComp-CUZ / ( #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | sequence Clear deltaF electron density map at position 291 suggests VAL rather than ALA. CLEAR ...sequence Clear deltaF electron density map at position 291 suggests VAL rather than ALA. CLEAR DELTAF ELECTRON DENSITY MAP AT POSITION 8 SUGGESTS ALA RATHER THAN GLY. |
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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: 2.37 Å3/Da / Density % sol: 47.76 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, Na cacodylate, Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: Haltia, T., (2003) BIOCHEM.J., 369, 77. | |||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 17, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. all: 272421 / Num. obs: 272421 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.05 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.63→1.65 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.252 / % possible all: 84.7 |
Reflection | *PLUS Lowest resolution: 40 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QNI Resolution: 1.6→29.83 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1693812.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.4278 Å2 / ksol: 0.372188 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 0.5 % / Rfactor obs: 0.241 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.389 / % reflection Rfree: 0.5 % / Rfactor Rwork: 0.322 |