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Yorodumi- PDB-1hcm: Cytochrome cd1 Nitrite Reductase, oxidised from from tetragonal c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hcm | ||||||
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Title | Cytochrome cd1 Nitrite Reductase, oxidised from from tetragonal crystals | ||||||
Components | CYTOCHROME CD1 NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ENZYME / NITRITE REDUCTASE | ||||||
Function / homology | Function and homology information hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | PARACOCCUS PANTOTROPHUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sjogren, T. / Hajdu, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: The Structure of an Alternative Form of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase Authors: Sjogren, T. / Hajdu, J. #1: Journal: Nature / Year: 1997 Title: Haem Ligand-Switching During Catalysis in Crystals of a Nitrogen Cycle Enzyme Authors: Williams, P.A. / Fulop, V. / Garman, E.F. / Saunders, N.F.W. / Ferguson, S.J. / Hajdu, J. #2: Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesis of Nitric Oxide by Cytochrome Cd1 Authors: Fulop, V. / Moir, J.W.B. / Saunders, N.F.W. / Ferguson, S.J. / Hajdu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hcm.cif.gz | 227.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hcm.ent.gz | 181.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hcm_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1hcm_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1hcm_validation.xml.gz | 44.5 KB | Display | |
Data in CIF | 1hcm_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/1hcm ftp://data.pdbj.org/pub/pdb/validation_reports/hc/1hcm | HTTPS FTP |
-Related structure data
Related structure data | 1h9xSC 1h9yC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 62546.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ORGANISM FORMERLY KNOWN AS THIOSPHAERA PANTOTROPHA / Source: (natural) PARACOCCUS PANTOTROPHUS (bacteria) / Cellular location: PERIPLASM / References: UniProt: Q9FCQ0, UniProt: P72181*PLUS #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: 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: 4.3 Å3/Da / Density % sol: 71.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 9 Details: HANGING DROP USING 2.1 M AMMONIUM SULPHATE AND 100 MM CHES PH 7.0 1 MM ASCORBATE AND 2.5 UM PMS FROM REDUCTION OF PROTEIN WAS ALSO PRESENT IN CRYSTALLISATION. CRYSTALS WERE GROWN UNDER ...Details: HANGING DROP USING 2.1 M AMMONIUM SULPHATE AND 100 MM CHES PH 7.0 1 MM ASCORBATE AND 2.5 UM PMS FROM REDUCTION OF PROTEIN WAS ALSO PRESENT IN CRYSTALLISATION. CRYSTALS WERE GROWN UNDER STRICTLY ANAEROBIC CONDITIONS. THE ENZYME WAS OXIDISED IN THE CRYSTAL BY ALLOWING AIR TO DIFFUSE INTO THE DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 1.0252 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0252 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 74676 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.28 / % possible all: 91.2 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 91.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H9X Resolution: 2.5→30 Å / SU B: 6.86 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IN SUBUNIT A RESIDUES A 1 - A 41 ARE DISORDERED STRUCTURE AND WERE NOT MODELLED. IN SUBUNIT B RESIDUES B 1 - B 38 ARE DISORDERED STRUCTURE AND WERE NOT MODELLED.
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Displacement parameters | Biso mean: 39.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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