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Yorodumi- PDB-2bii: crystal structure of nitrate-reducing fragment of assimilatory ni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bii | ||||||
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Title | crystal structure of nitrate-reducing fragment of assimilatory nitrate reductase from Pichia angusta | ||||||
Components | NITRATE REDUCTASE [NADPH] | ||||||
Keywords | OXIDOREDUCTASE / FAD / FLAVOPROTEIN / HEME / MOLYBDENUM / NADP / NITRATE ASSIMILATION | ||||||
Function / homology | Function and homology information nitrate reductase (NADPH) / nitrate reductase (NADPH) activity / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / nitrate assimilation / nitric oxide biosynthetic process / FAD binding / heme binding / mitochondrion Similarity search - Function | ||||||
Biological species | PICHIA ANGUSTA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Fischer, K. / Barbier, G. / Hecht, H.-J. / Mendel, R.R. / Campbell, W.H. / Schwarz, G. | ||||||
Citation | Journal: Plant Cell / Year: 2005 Title: Structural Basis of Eukaryotic Nitrate Reduction: Crystal Structures of the Nitrate Reductase Active Site Authors: Fischer, K. / Barbier, G. / Hecht, H.-J. / Mendel, R.R. / Campbell, W.H. / Schwarz, G. | ||||||
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 | 2bii.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bii.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 2bii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/2bii ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2bii | HTTPS FTP |
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-Related structure data
Related structure data | 2bihSC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48564.398 Da / Num. of mol.: 2 Fragment: MOCO-BINDING DOMAIN, DIMERIZATION DOMAIN, RESIDUES 1-13,20-478 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PICHIA ANGUSTA (fungus) / Plasmid: SNAR1-PPICZB / Production host: PICHIA PASTORIS (fungus) / Strain (production host): Y-11430 / References: UniProt: P49050, EC: 1.7.1.2 |
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-Non-polymers , 5 types, 810 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE AUTHORS INDICATE THAT THE CONFLICT DESCRIBED BELOW IS PROBABLY DUE TO ERROR IN THE SEQUENCE ...THE AUTHORS INDICATE THAT THE CONFLICT DESCRIBED BELOW IS PROBABLY DUE TO ERROR IN THE SEQUENCE DATABASE ANNOTATION |
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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: 2.9 Å3/Da / Density % sol: 57.3 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.005 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 23, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. obs: 2235039 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BIH Resolution: 1.7→87.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.529 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→87.71 Å
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Refine LS restraints |
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