[English] 日本語
Yorodumi- PDB-1oah: Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oah | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774: The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA). | |||||||||
Components | CYTOCHROME C NITRITE REDUCTASE | |||||||||
Keywords | REDUCTASE / CYTOCHROME C / NITRITE REDUCTASE / NITROGEN CYCLE / RESPIRATORY NITRITE AMMONIFICATION | |||||||||
Function / homology | Function and homology information nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / : / periplasmic space / metal ion binding Similarity search - Function | |||||||||
Biological species | DESULFOVIBRIO DESULFURICANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Cunha, C.A. / Macieira, S. / Dias, J.M. / Almeida, G. / Goncalves, L.L. / Costa, C. / Lampreia, J. / Huber, R. / Moura, J.J.G. / Moura, I. / Romao, M.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Cytochrome C Nitrite Reductase from Desulfovibrio Desulfuricans Atcc 27774. The Relevance of the Two Calcium Sites in the Structure of the Catalytic Subunit (Nrfa) Authors: Cunha, C.A. / Macieira, S. / Dias, J.M. / Almeida, G. / Goncalves, L.L. / Costa, C. / Lampreia, J. / Huber, R. / Moura, J.J.G. / Moura, I. / Romao, M.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1oah.cif.gz | 226.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1oah.ent.gz | 181.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oah ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oah | HTTPS FTP |
---|
-Related structure data
Related structure data | 1qdbS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 59232.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) References: UniProt: Q8VNU2, nitrite reductase (cytochrome; ammonia-forming) |
---|
-Non-polymers , 5 types, 519 molecules
#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | RESIDUE 519 PRESENT IN THE ELECTRON DENSITY NOT SEQUENCE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47 % Description: THE STRUCTURE WAS SOLVED COMBINING MAD PHASES WITH A MOLECULAR REPLACEMENT SOLUTION. THE MAD DATA SET (TO 2.5 ANGSTROMS RESOLUTION) WAS COLLECTED AT BEAMLINE BM14 WITH A MAR345 DETECTOR ...Description: THE STRUCTURE WAS SOLVED COMBINING MAD PHASES WITH A MOLECULAR REPLACEMENT SOLUTION. THE MAD DATA SET (TO 2.5 ANGSTROMS RESOLUTION) WAS COLLECTED AT BEAMLINE BM14 WITH A MAR345 DETECTOR AND A DATASET UP TO 2.3 ANGSTROMS WAS COLLECTED AT ID14-EH4 WITH A ADSC DETECTOR. | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% W/V PEG 3350, CACL2 0.2M, HEPES PH7.5, 0.1M, 3-(DECYL-METHYLAMMONIUM)PROPANE-1-SULFONATE (ZWITTERGENT 3-10) AS ADDITIVE, pH 7.50 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.7403,1.7390,0.9919, 0.932 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.3→84.5 Å / Num. obs: 53690 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.2 / % possible all: 89.8 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 51633 / % possible obs: 97.3 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 89.8 % |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD, molecular replacement Starting model: PDB ENTRY 1QDB Resolution: 2.3→20 Å / SU B: 6.381 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.214 Details: RESIDUES 325 - 331 ARE MISSING IN CHAIN A BECAUSE NO ELECTRON DENSITY CORRESPONDING TO THESE RESIDUES COULD BE SEEN IN THE ELECTRON DENSITY MAPS.
| |||||||||||||||||||||
Displacement parameters | Biso mean: 27.7 Å2
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| |||||||||||||||||||||
Refine LS restraints | *PLUS
|