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Yorodumi- PDB-1gs8: Crystal structure of mutant D92N Alcaligenes xylosoxidans Nitrite... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gs8 | ||||||
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Title | Crystal structure of mutant D92N 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 / ferroxidase activity / nitrate assimilation / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ALCALIGENES XYLOSOXIDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 |
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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gs8.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gs8.ent.gz | 62.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gs8_validation.pdf.gz | 368 KB | Display | wwPDB validaton report |
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Full document | 1gs8_full_validation.pdf.gz | 370.6 KB | Display | |
Data in XML | 1gs8_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1gs8_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/1gs8 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/1gs8 | HTTPS FTP |
-Related structure data
Related structure data | 1gs6C 1gs7C 1ndtS 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
#1: Protein | Mass: 36569.543 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: PENIRD92N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: O68601, EC: 1.7.99.3, nitrite reductase (NO-forming) | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.02 % Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.5 / Details: 40-50% PEG-MME 550, 10MM ZNSO4, 0.1M MES PH 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: vapor diffusion, sitting drop / pH: 7.1 | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2000 / 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: 1.9→20 Å / Num. obs: 35114 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
Reflection | *PLUS % possible obs: 100 % / Num. measured all: 185774 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NDT Resolution: 1.9→68.97 Å / SU B: 3.674 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Refinement step | Cycle: LAST / Resolution: 1.9→68.97 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.171 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.016 |