+Open data
-Basic information
Entry | Database: PDB / ID: 1h9x | ||||||
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Title | Cytochrome cd1 Nitrite Reductase, reduced form | ||||||
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: 2.1 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 | 1h9x.cif.gz | 236.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h9x.ent.gz | 187.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h9x_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 1h9x_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1h9x_validation.xml.gz | 47.4 KB | Display | |
Data in CIF | 1h9x_validation.cif.gz | 68.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/1h9x ftp://data.pdbj.org/pub/pdb/validation_reports/h9/1h9x | HTTPS FTP |
-Related structure data
Related structure data | 1h9yC 1hcmC 1aofS C: citing same article (ref.) 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 , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 643 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NHE / | #5: Chemical | #6: 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 ASCORMBATE AND 2.5 UM PMS FROM REDUCTION OF PROTEIN WAS ALSO PRESENT IN CRYSTALLISATION. | ||||||||||||||||||||||||||||||
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: Jun 6, 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: 2.1→30 Å / Num. obs: 126324 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.224 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AOF, D1 DOMAIN DIMER Resolution: 2.1→30 Å / SU B: 3.53 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.141 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: 28.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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