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Yorodumi- PDB-1oe1: Atomic Resolution Structure of the Wildtype Native Nitrite Reduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oe1 | |||||||||
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Title | Atomic Resolution Structure of the Wildtype Native Nitrite Reductase from Alcaligenes xylosoxidans | |||||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | |||||||||
Keywords | REDUCTASE / DENITRIFICATION / NITRITE REDUCTASE | |||||||||
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: 1.04 Å | |||||||||
Authors | Ellis, M.J. / Dodd, F.E. / Hasnain, S.S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Atomic Resolution Structures of Native Copper Nitrite Reductase from Alcaligenes Xylosoxidans and the Active Site Mutant Asp92Glu Authors: Ellis, M.J. / Dodd, F.E. / 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 | 1oe1.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oe1.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 1oe1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oe1_validation.pdf.gz | 377 KB | Display | wwPDB validaton report |
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Full document | 1oe1_full_validation.pdf.gz | 382.2 KB | Display | |
Data in XML | 1oe1_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1oe1_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/1oe1 ftp://data.pdbj.org/pub/pdb/validation_reports/oe/1oe1 | HTTPS FTP |
-Related structure data
Related structure data | 1oe2C 1oe3C 1hauS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36553.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: WILDTYPE NATIVE PROTEIN FROM ALCAILGENES XYLOSOXIDANS Source: (natural) ALCALIGENES XYLOSOXIDANS (bacteria) / References: UniProt: O68601 | ||||
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#2: Chemical | #3: Chemical | ChemComp-PG4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.2 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 40-50% PEG-MME 550, 0.1M MES PH 6.5, 10MM CUSO4 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
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: PX14.2 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→60 Å / Num. obs: 167110 / % possible obs: 96.6 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 93.1 |
Reflection | *PLUS Lowest resolution: 60 Å / Num. measured all: 1766001 |
Reflection shell | *PLUS % possible obs: 93.1 % / Num. unique obs: 7735 / Num. measured obs: 17252 / Rmerge(I) obs: 0.333 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HAU Resolution: 1.04→60 Å / Num. parameters: 27952 / Num. restraintsaints: 33870 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: NO GEOMETRIC OR ADP RESTRAINTS APPLIED TO COPPER ATOMS. DISORDERED SIDE CHAINS INCLUDED DUE TO KNOWN SEQUENCE
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 18 / Occupancy sum non hydrogen: 3106 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→60 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELX / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.13 / Rfactor Rwork: 0.117 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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