[English] 日本語
Yorodumi- PDB-1gs6: Crystal structure of M144A mutant of Alcaligenes xylosoxidans Nit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gs6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of M144A mutant of Alcaligenes xylosoxidans Nitrite Reductase | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / MULTICOPPER / PERIPLASMIC | ||||||
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 | ALCALIGENES XYLOSOXIDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ellis, M.J. / Prudencio, M. / Dodd, F.E. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Biochemical and Crystallographic Studies of the met144Ala, Asp92Asn and His254Phe Mutants of the Nitrite Reductase from Alcaligenes Xylosoxidans Provide Insight Into the Enzyme Mechanism. Authors: Ellis, M.J. / Prudencio, M. / Dodd, F.E. / Strange, R.W. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gs6.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gs6.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gs6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/1gs6 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/1gs6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1gs7C 1gs8C 1ndtS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36510.410 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ALCALIGENES XYLOSOXIDANS (bacteria) / Strain: N.C.I.M.B. 11015 / Plasmid: PENIRM144A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: O68601, EC: 1.7.99.3, nitrite reductase (NO-forming) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.6 % / Description: COLLECTED USING OSCILLATION METHOD |
---|---|
Crystal grow | pH: 8.5 Details: 30% PEG 4000, 0.1M MGCL2, 0.1M TRIS-HCL PH8.5, TEMP GRADIENT 4-32 DEGREES C, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 294 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 1999 / Details: RH COATED SI MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 27656 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDN ENTRY 1NDT Resolution: 2.2→60 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.786 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→60 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|