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Yorodumi- PDB-5jrv: Crystal structure of Fe(II) NO-bound H-NOX protein from C. subter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jrv | ||||||
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Title | Crystal structure of Fe(II) NO-bound H-NOX protein from C. subterraneus | ||||||
Components | Methyl-accepting chemotaxis protein | ||||||
Keywords | SIGNALING PROTEIN / Heme-based methyl-accepting chemotaxis protein Gas binding Signaling protein | ||||||
Function / homology | Function and homology information lysozyme activity / heme binding / signal transduction / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å | ||||||
Authors | Bruegger, J. / Hespen, C. / Phillips-Piro, C.M. / Marletta, M.A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Structural and Functional Evidence Indicates Selective Oxygen Signaling in Caldanaerobacter subterraneus H-NOX. Authors: Hespen, C.W. / Bruegger, J.J. / Phillips-Piro, C.M. / 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 | 5jrv.cif.gz | 98.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jrv.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jrv_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5jrv_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5jrv_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5jrv_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/5jrv ftp://data.pdbj.org/pub/pdb/validation_reports/jr/5jrv | HTTPS FTP |
-Related structure data
Related structure data | 5jruC 5jrxC 1u55S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22047.502 Da / Num. of mol.: 2 / Fragment: UNP residues 1-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria) Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: Tar4, TTE0680 / Production host: Escherichia coli (E. coli) / Strain (production host): RP523 (DE3) / References: UniProt: Q8RBX6 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IOD / | #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: 2.6 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Anaerobically grown under Argon. 20 mg/mL protein with well condition of 0.15 M NaI, 25% PEG3350. |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999919 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999919 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 32785 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.5 Å2 / CC1/2: 0.909 / Rmerge(I) obs: 0.093 / Rsym value: 0.087 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.67 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U55 Resolution: 1.953→49.979 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.18 / 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: 1.953→49.979 Å
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Refine LS restraints |
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LS refinement shell |
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