[English] 日本語
Yorodumi- PDB-2xx1: STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xx1 | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / PROTON CHANNEL / DENITRIFICATION | ||||||
Function / homology | Function and homology information denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ACHROMOBACTER XYLOSOXIDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Antonyuk, S.V. / Leferink, N.G.H. / Han, C. / Heyes, D.J. / Rigby, S.E.J. / Hough, M.A. / Eady, R.R. / Scrutton, N.S. / Hasnain, S.S. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase. Authors: Leferink, N.G.H. / Han, C. / Antonyuk, S.V. / Heyes, D.J. / Rigby, S.E.J. / Hough, M.A. / Eady, R.R. / Scrutton, N.S. / Hasnain, S.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xx1.cif.gz | 390.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xx1.ent.gz | 320.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/2xx1 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xx1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2xwzC 2xx0C 2xxfC 2jl0 C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 36544.488 Da / Num. of mol.: 6 / Fragment: RESIDUES 26-360 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Strain: IW2 IWASAKI / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O68601, nitrite reductase (NO-forming) #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-NO2 / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 114 TO SER ENGINEERED RESIDUE IN CHAIN B, ASN 114 TO SER ...ENGINEERED | Sequence details | RESIDUE N90 WAS MUTATED TO SERINE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 6.37 Å3/Da / Density % sol: 80 % / Description: NONE |
---|---|
Crystal grow | pH: 4.6 / Details: 1.8 M AMMONIUM SULPHATE IN CITRATE BUFFER, PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99187 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→43.7 Å / Num. obs: 109627 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.35 |
Reflection shell | Resolution: 3→3.17 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.54 / % possible all: 98.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JL0 2jl0 Resolution: 3→42.99 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 10.862 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.18 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→42.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|