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Yorodumi- PDB-4n4m: Kuenenia stuttgartiensis hydroxylamine oxidoreductase soaked in p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n4m | |||||||||
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Title | Kuenenia stuttgartiensis hydroxylamine oxidoreductase soaked in phenyl hydrazine | |||||||||
Components | hydroxylamine oxidoreductase | |||||||||
Keywords | OXIDOREDUCTASE / C-type cytochrome | |||||||||
Function / homology | Function and homology information hydroxylamine oxidase / anaerobic respiration, using ammonium as electron donor / hydroxylamine oxidoreductase activity / anammoxosome / protein homotrimerization / nitric oxide biosynthetic process / heme binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Candidatus Kuenenia stuttgartiensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | |||||||||
Authors | Maalcke, W.J. / Dietl, A. / Marritt, S.J. / Butt, J.N. / Jetten, M.S.M. / Keltjens, J.T. / Barends, T.R.M.B. / Kartal, B. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural Basis of Biological NO Generation by Octaheme Oxidoreductases. Authors: Maalcke, W.J. / Dietl, A. / Marritt, S.J. / Butt, J.N. / Jetten, M.S. / Keltjens, J.T. / Barends, T.R. / Kartal, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n4m.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n4m.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/4n4m ftp://data.pdbj.org/pub/pdb/validation_reports/n4/4n4m | HTTPS FTP |
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-Related structure data
Related structure data | 4n4jSC 4n4kC 4n4lC 4n4nC 4n4oC 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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Details | Covalent trimer confirmed by SDS-PAGE, analytical ultracentrifugation, and gel filtration |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56543.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Candidatus Kuenenia stuttgartiensis (bacteria) References: UniProt: Q1PX48, hydroxylamine oxidase |
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-Non-polymers , 5 types, 288 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PHZ / | #5: Chemical | ChemComp-HEC / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.3 M ammonium sulfate, 0.05-0.10 M sodium phosphate, pH 7.4, detergent additive cyclohexylbutanoyl-N-hydroxyethylglucamide (C-HEGA-10), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.05 Å / Num. all: 41094 / Num. obs: 41094 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.1→2.2 Å / Rmerge(I) obs: 0.455 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4N4J Resolution: 2.1→46.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.674 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.141 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.645 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.05 Å
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Refine LS restraints |
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