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Yorodumi- PDB-4iuk: Crystal structure of NreA of Staphylococcus carnosus with bound n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iuk | ||||||
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Title | Crystal structure of NreA of Staphylococcus carnosus with bound nitrate | ||||||
Components | NreA protein | ||||||
Keywords | Nitrate-binding protein / GAF domain / Nitrate sensor / Staphylococcus / Nitrate binding / Nitrate / Cytosolic | ||||||
Function / homology | GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / NITRATE ION / NreA protein Function and homology information | ||||||
Biological species | Staphylococcus carnosus subsp. carnosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Stehle, T. / Niemann, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: The NreA Protein Functions as a Nitrate Receptor in the Staphylococcal Nitrate Regulation System. Authors: Niemann, V. / Koch-Singenstreu, M. / Neu, A. / Nilkens, S. / Gotz, F. / Unden, G. / Stehle, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iuk.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iuk.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 4iuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iuk_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 4iuk_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 4iuk_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 4iuk_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/4iuk ftp://data.pdbj.org/pub/pdb/validation_reports/iu/4iuk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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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
#1: Protein | Mass: 18854.338 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus carnosus subsp. carnosus (bacteria) Strain: TM300 / Gene: nreA, Sca_1890, SCA_1890 / Production host: Escherichia coli (E. coli) / References: UniProt: B9DL91 #2: Chemical | #3: 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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 12.5 % (w/v) PEG 1.000, 12.5 % (w/v) PEG 3350, 12.5 % (v/v) 2-methyl-2,4-pentanediol, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M bicine/Trizma ...Details: 12.5 % (w/v) PEG 1.000, 12.5 % (w/v) PEG 3350, 12.5 % (v/v) 2-methyl-2,4-pentanediol, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M bicine/Trizma base, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 9, 2011 |
Radiation | Monochromator: toroidal focused Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→42.83 Å / Num. obs: 14713 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.35→2.41 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→42.83 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 26.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→42.83 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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