+Open data
-Basic information
Entry | Database: PDB / ID: 4xyd | ||||||
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Title | Nitric oxide reductase from Roseobacter denitrificans (RdNOR) | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Nitric oxide reductase / membrane protein / heme copper oxidase superfamily | ||||||
Function / homology | Function and homology information nitric oxide reductase (cytochrome c) / nitric oxide reductase activity / cytochrome-c oxidase activity / : / aerobic respiration / membrane => GO:0016020 / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Roseobacter denitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Crow, A. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans. Authors: Crow, A. / Matsuda, Y. / Arata, H. / Oubrie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xyd.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xyd.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xyd_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4xyd_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4xyd_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 4xyd_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/4xyd ftp://data.pdbj.org/pub/pdb/validation_reports/xy/4xyd | HTTPS FTP |
-Related structure data
Related structure data | 3o0rS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.23388 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 51404.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Roseobacter denitrificans (strain ATCC 33942 / OCh 114) (bacteria) References: UniProt: Q16A04, nitric oxide reductase (cytochrome c) |
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#2: Protein | Mass: 16853.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Roseobacter denitrificans (strain ATCC 33942 / OCh 114) (bacteria) References: UniProt: Q16A03, nitric oxide reductase (cytochrome c) |
-Non-polymers , 7 types, 23 molecules
#3: Chemical | #4: Chemical | ChemComp-UNL / | Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-FE / | #7: Chemical | ChemComp-HEC / | #8: Chemical | ChemComp-CU / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Crystallization reagent composed of 100 mM MOPS pH 7.6, 28 % (w/v) PEG 600. Protein solution 8mg/ml 20 mM MOPS pH 7.2, 100 mM NaCl, 0.4 % (w/v) nonyl-B-D-glucopyranoside. Mixed 1:1 in sitting drop at 4C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→53.36 Å / Num. obs: 25236 / % possible obs: 97.2 % / Redundancy: 6.7 % / Rsym value: 0.102 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.85→3 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.362 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3O0R Resolution: 2.85→53.36 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.875 / SU B: 13.74 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.58 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.85 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.866 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→53.36 Å
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Refine LS restraints |
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