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Yorodumi- PDB-1haw: X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1haw | ||||||
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Title | X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 A RESOLUTION | ||||||
Components | DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / REDUCTASE / COPPER / BLUE COPPER | ||||||
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 XYLOSOXYDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ellis, M.J. / Dodd, F.E. / Strange, R.W. / Prudencio, M. / Sawerseady, R.R. / Hasnain, S.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: X-Ray Structure of a Blue Copper Nitrite Reductase at High Ph and in Copper-Free Form at 1.9 A Resolution Authors: Ellis, M.J. / Dodd, F.E. / Strange, R.W. / Prudencio, M. / Sawers, G. / Eady, R.R. / Hasnain, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1haw.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1haw.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 1haw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/1haw ftp://data.pdbj.org/pub/pdb/validation_reports/ha/1haw | HTTPS FTP |
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-Related structure data
Related structure data | 1hauC 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: 36570.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ALCALIGENES XYLOSOXYDANS (bacteria) / Cellular location: PERIPLASM / Strain: XYLOSOXIDANS References: UniProt: O68601, EC: 1.7.99.3, nitrite reductase (NO-forming) |
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#2: Chemical | ChemComp-CU1 / |
#3: 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: 2.87 Å3/Da / Density % sol: 56.85 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 30% PEG 4K, 0.1M MAGNESIUM CHLORIDE, 0.1M TRIS-HCL PH8.5, pH 8.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1999 / Details: TORROIDAL MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→52.705 Å / Num. obs: 29659 / % possible obs: 93.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 15.67 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.2 / % possible all: 83.4 |
Reflection | *PLUS Num. measured all: 133607 |
Reflection shell | *PLUS % possible obs: 83.4 % / Num. unique obs: 3854 / Num. measured obs: 9181 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NDT MONOMER Resolution: 1.9→20 Å / SU B: 2.32 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12 Details: RESIDUES WITH ZERO OCCUPANCY, NOT SEEN IN THE DENSITY MAPS
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Displacement parameters | Biso mean: 25.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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