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Yorodumi- PDB-5ohf: Globin sensor domain of AfGcHK (FeIII form) in complex with cyani... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ohf | ||||||||||||
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Title | Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide, partially reduced | ||||||||||||
Components | Globin-coupled histidine kinase | ||||||||||||
Keywords | TRANSFERASE / Heme / Sensor protein / Oxygen sensor / Globin sensor domain / globin domain / cyanide | ||||||||||||
Function / homology | Function and homology information peptidyl-histidine phosphorylation / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / oxygen binding / heme binding / protein homodimerization activity / ATP binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Anaeromyxobacter sp. | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||||||||
Authors | Skalova, T. / Kolenko, P. / Dohnalek, J. / Stranava, M. / Martinkova, M. | ||||||||||||
Funding support | Czech Republic, 3items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction. Authors: Stranava, M. / Man, P. / Skalova, T. / Kolenko, P. / Blaha, J. / Fojtikova, V. / Martinek, V. / Dohnalek, J. / Lengalova, A. / Rosulek, M. / Shimizu, T. / Martinkova, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ohf.cif.gz | 306.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ohf.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ohf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ohf_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 5ohf_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 5ohf_validation.xml.gz | 62.3 KB | Display | |
Data in CIF | 5ohf_validation.cif.gz | 86.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/5ohf ftp://data.pdbj.org/pub/pdb/validation_reports/oh/5ohf | HTTPS FTP |
-Related structure data
Related structure data | 5oheSC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 18370.861 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaeromyxobacter sp. (strain Fw109-5) (bacteria) Gene: gchK, Anae109_2438 / Plasmid: pET21c(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7HD43, histidine kinase |
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-Non-polymers , 5 types, 1038 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-CYN / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / | #6: 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: 2.27 Å3/Da / Density % sol: 46 % Description: Crystal shape - red wedge block 300x80x80 um; the crystal was soaked for 15 min in a maternal drop containing additionally 10 mM sodium dithionite. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 20.7% (w/v) PEG3350, 200 mM MgCl2, 0.01 M KCN, 7.5% (v/v) glycerol, 0.1 M MMT buffer system (DL-Malic acid, MES monohydrate, Tris, NaOH, HCl), pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.17 Å / Num. obs: 127077 / % possible obs: 100 % / Observed criterion σ(I): -3.7 / Redundancy: 7.3 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6192 / CC1/2: 0.844 / Rpim(I) all: 0.442 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OHE Resolution: 1.8→49.17 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 2.748 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→49.17 Å
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