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Yorodumi- PDB-4u99: Crystal structure of an H-NOX protein from S. oneidensis in the F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u99 | ||||||
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Title | Crystal structure of an H-NOX protein from S. oneidensis in the Fe(II) ligation state, Q154A/Q155A/K156A mutant | ||||||
Components | NO-binding heme-dependent sensor protein | ||||||
Keywords | SIGNALING PROTEIN / H-NOX / hemoprotein / gas sensor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Herzik Jr., M.A. / Jonnalagadda, R. / Kuriyan, J. / Marletta, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural insights into the role of iron-histidine bond cleavage in nitric oxide-induced activation of H-NOX gas sensor proteins. Authors: Herzik, M.A. / Jonnalagadda, R. / Kuriyan, J. / Marletta, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u99.cif.gz | 238.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u99.ent.gz | 198.1 KB | Display | PDB format |
PDBx/mmJSON format | 4u99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u99_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4u99_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4u99_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 4u99_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/4u99 ftp://data.pdbj.org/pub/pdb/validation_reports/u9/4u99 | HTTPS FTP |
-Related structure data
Related structure data | 4u9bC 4u9gC 4u9jC 4u9kC 3tf8S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21157.244 Da / Num. of mol.: 2 / Mutation: Q154A, Q155A, K156A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_2144 / Plasmid: pET20 / Production host: Escherichia coli (E. coli) / Strain (production host): RP523(DE3) / References: UniProt: Q8EF49 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NA / | #5: 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: 4.55 Å3/Da / Density % sol: 72.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: Obtained by equilibrating a 2 uL drop of 1:1 protein:reservoir against a 700 uL reservoir containing 1.6-1.9 M DL-malic acid (pH 7.3). For cryoprotection, 2 uL of mother liquor containing ...Details: Obtained by equilibrating a 2 uL drop of 1:1 protein:reservoir against a 700 uL reservoir containing 1.6-1.9 M DL-malic acid (pH 7.3). For cryoprotection, 2 uL of mother liquor containing 10% glycerol was added directly to the drop and crystals were serial transferred into mother liquor solution containing 5, 7.5 and 10% glycerol prior to flash freezing in liquid nitrogen. Crystal growth and manipulation was performed anaerobically. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.882 Å / Num. obs: 102223 / % possible obs: 98.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 42.51 Å2 / Rmerge(I) obs: 0.021 / Net I/σ(I): 0.208 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.4 / % possible all: 97.9 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TF8 Resolution: 2→47.88 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.01 / 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→47.88 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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