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Yorodumi- PDB-6bdd: Crystal structure of Fe(II) unliganded H-NOX protein from K. algicida -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bdd | ||||||
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Title | Crystal structure of Fe(II) unliganded H-NOX protein from K. algicida | ||||||
Components | 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase | ||||||
Keywords | SIGNALING PROTEIN / Nitric oxide signaling / heme nitric oxide/oxygen sensing protein | ||||||
Function / homology | Heme NO-binding / H-NOX domain superfamily / Haem-NO-binding / NO signalling/Golgi transport ligand-binding domain superfamily / heme binding / PROTOPORPHYRIN IX CONTAINING FE / 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase Function and homology information | ||||||
Biological species | Kordia algicida OT-1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å | ||||||
Authors | Bruegger, J.J. / Hespen, C.W. / Marletta, M.A. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Native Alanine Substitution in the Glycine Hinge Modulates Conformational Flexibility of Heme Nitric Oxide/Oxygen (H-NOX) Sensing Proteins. Authors: Hespen, C.W. / Bruegger, J.J. / Guo, Y. / 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 | 6bdd.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bdd.ent.gz | 72.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bdd_validation.pdf.gz | 777 KB | Display | wwPDB validaton report |
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Full document | 6bdd_full_validation.pdf.gz | 777.1 KB | Display | |
Data in XML | 6bdd_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 6bdd_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/6bdd ftp://data.pdbj.org/pub/pdb/validation_reports/bd/6bdd | HTTPS FTP |
-Related structure data
Related structure data | 6bdeC 4u99S 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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Unit cell |
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-Components
#1: Protein | Mass: 21284.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kordia algicida OT-1 (bacteria) / Gene: KAOT1_17313 / Production host: Escherichia coli (E. coli) / References: UniProt: A9DSJ8 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.04 % / Description: Rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 0.3 M LiCl, 34% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.17 Å / Num. obs: 15750 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 34.58 Å2 / CC1/2: 0.616 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.78 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 692 / % possible all: 91.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U99 Resolution: 1.901→44.17 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.36 Å2 / Biso mean: 42.7677 Å2 / Biso min: 19.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.901→44.17 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 2.795 Å / Origin y: -6.862 Å / Origin z: -2.044 Å
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Refinement TLS group |
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