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Yorodumi- PDB-2y1a: Crystal structure of Achromobacter cycloclastes Cu nitrite reduct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y1a | ||||||
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Title | Crystal structure of Achromobacter cycloclastes Cu nitrite reductase with bound NO | ||||||
Components | COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / 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 CYCLOCLASTES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hough, M.A. / Antonyuk, S.V. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2011 Title: Monitoring and Validating Active Site Redox States in Protein Crystals. Authors: Antonyuk, S.V. / Hough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y1a.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y1a.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 2y1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/2y1a ftp://data.pdbj.org/pub/pdb/validation_reports/y1/2y1a | HTTPS FTP |
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-Related structure data
Related structure data | 2y3qC 2bw4S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37059.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ACHROMOBACTER CYCLOCLASTES (bacteria) / References: UniProt: P25006, nitrite reductase (NO-forming) |
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-Non-polymers , 5 types, 243 molecules
#2: Chemical | #3: Chemical | ChemComp-NO / | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: 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 Å3/Da / Density % sol: 36.6 % / Description: NONE |
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Crystal grow | pH: 4.75 Details: 1.6M AMMONIUM SULPHATE, 100MM SODIUM ACETATE PH 4.75 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.37 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.37 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→26.4 Å / Num. obs: 19807 / % possible obs: 93.2 % / Observed criterion σ(I): 0.1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 6.7 / % possible all: 58.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BW4 Resolution: 1.95→26.41 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.192 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. STRUCTURE IN SPECTROSCOPICALLY VALIDATED REDOX STATE.
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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: 15.991 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→26.41 Å
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Refine LS restraints |
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