+Open data
-Basic information
Entry | Database: PDB / ID: 1e2r | ||||||
---|---|---|---|---|---|---|---|
Title | CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / DENITRIFICATION / ELECTRON TRANSPORT / PERIPLASMIC / CYANIDE | ||||||
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 DENITRIFICANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Fulop, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus. Authors: Jafferji, A. / Allen, J.W. / Ferguson, S.J. / Fulop, V. #1: Journal: J.Mol.Biol. / Year: 1997 Title: Cytochrome Cd1 Structure: Unusual Haem Environments in a Nitrite Reductase and Analysis of Factors Contributing to Beta-Propeller Folds Authors: Baker, S.C. / Saunders, N.F.W. / Willis, A.C. / Ferguson, S.J. / Hajdu, J. / Fulop, V. #2: 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. #3: Journal: Cell(Cambridge,Mass.) / Year: 1995 Title: The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesys of Nitric Oxide by Cytochrome Cd1 Authors: Fulop, V. / Moir, J.W.B. / Ferguson, S.J. / Hajdu, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1e2r.cif.gz | 253.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1e2r.ent.gz | 202.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e2r_validation.pdf.gz | 720.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1e2r_full_validation.pdf.gz | 731.1 KB | Display | |
Data in XML | 1e2r_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 1e2r_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/1e2r ftp://data.pdbj.org/pub/pdb/validation_reports/e2/1e2r | HTTPS FTP |
-Related structure data
Related structure data | 1aofS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.721099, 0.545573, 0.427044), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 62603.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: SUBSP. PARACOCCUS PANTOTROPHUS FORMALLY KNOWN AS THIOSPHAERA PANTOTROPHA Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: PERIPLASM References: UniProt: P72181, nitrite reductase (NO-forming), hydroxylamine reductase |
---|
-Non-polymers , 5 types, 1351 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: 2.3 M AMMONIUM SULFATE, 50MM POTASSIUM PHOSPHATE, PH 7.0, AND CRYOPROTECTANT 15% GLYCEROL | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.83 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.83 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→25 Å / Num. obs: 156509 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.145 / % possible all: 96.7 |
Reflection | *PLUS Num. measured all: 599187 / Rmerge(I) obs: 0.081 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AOF Resolution: 1.59→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.59→1.62 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.23 |