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Yorodumi- PDB-1nds: CRYSTALLOGRAPHIC STRUCTURE OF A SUBSTRATE BOUND BLUE COPPER NITRI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nds | ||||||
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Title | CRYSTALLOGRAPHIC STRUCTURE OF A SUBSTRATE BOUND BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS | ||||||
Components | NITRITE REDUCTASE | ||||||
Keywords | REDUCTASE / BLUE COPPER NITRITE REDUCTASE / COPPER PROTEIN / NITRITE REDUCTION | ||||||
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: 2.8 Å | ||||||
Authors | Dodd, F.E. / Hasnain, S.S. / Abraham, Z.H.L. / Eady, R.R. / Smith, B.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Structures of a blue-copper nitrite reductase and its substrate-bound complex. Authors: Dodd, F.E. / Hasnain, S.S. / Abraham, Z.H. / Eady, R.R. / Smith, B.E. #1: Journal: Biochem.J. / Year: 1993 Title: Purification and Characterization of the Dissimilatory Nitrite Reductase from Alcaligenes Xylosoxidans Subsp. Xylosoxidans (N.C.I.M.B. 11015): Evidence for the Presence of Both Type 1 and Type 2 Copper Centers Authors: Abraham, Z.H. / Lowe, D.J. / Smith, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nds.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nds.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 1nds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nds_validation.pdf.gz | 398.1 KB | Display | wwPDB validaton report |
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Full document | 1nds_full_validation.pdf.gz | 400.9 KB | Display | |
Data in XML | 1nds_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 1nds_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1nds ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1nds | HTTPS FTP |
-Related structure data
Related structure data | 1ndrC 1afn 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34441.711 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: BACTERIAL / Source: (natural) Achromobacter xylosoxidans (bacteria) / Strain: NCIMB 11015 / References: UniProt: P81445, EC: 1.7.99.3 #2: Chemical | ChemComp-CU / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: MODEL WITHOUT WATERS | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 4.6 Details: 28% PEG 4000, 0.1M SODIUM ACETATE, PH 4.6, 4 DEGREES C, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: used to seeding | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 286 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1996 / Details: FOCUSSING PLATINUM COATED : TORROID |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→53 Å / Num. obs: 24358 / % possible obs: 91.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 6.3 / % possible all: 82.5 |
Reflection | *PLUS Num. measured all: 76663 |
Reflection shell | *PLUS % possible obs: 82.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NITRITE REDUCTASE PDB CODE 1AFN 1afn Resolution: 2.8→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: R-FREE / σ(F): 2 Details: THIS IS AN ALPHA CARBON ENTRY. THE SIDE CHAINS FOR HIS 95 HIS 100, HIS 135, CYS 136, HIS 145, HIS 306 AND ONE SOLVENT MOLECULE, HOH 503 WHICH ARE INVOLVED IN COPPER COORDINATION ARE ALSO ...Details: THIS IS AN ALPHA CARBON ENTRY. THE SIDE CHAINS FOR HIS 95 HIS 100, HIS 135, CYS 136, HIS 145, HIS 306 AND ONE SOLVENT MOLECULE, HOH 503 WHICH ARE INVOLVED IN COPPER COORDINATION ARE ALSO INCLUDED. SIDE CHAINS FOR MET 150 ARE ALSO INCLUDED.
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Displacement parameters | Biso mean: 10.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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