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Yorodumi- PDB-4hu4: Crystal structure of EAL domain of the E. coli DosP - dimeric form -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hu4 | ||||||
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Title | Crystal structure of EAL domain of the E. coli DosP - dimeric form | ||||||
Components | Oxygen sensor protein DosP | ||||||
Keywords | SIGNALING PROTEIN / HYDROLASE / EAL domain / cyclic di-GMP phosphodiesterase / TIM-barrel / EcDos / direct oxygen sensor | ||||||
Function / homology | Function and homology information cyclic-guanylate-specific phosphodiesterase / cyclic-guanylate-specific phosphodiesterase activity / response to oxygen levels / oxygen sensor activity / heme binding / magnesium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Tarnawski, M. / Barends, T.R.M. / Hartmann, E. / Schlichting, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structures of the catalytic EAL domain of the Escherichia coli direct oxygen sensor. Authors: Tarnawski, M. / Barends, T.R. / Hartmann, E. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hu4.cif.gz | 111.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hu4.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 4hu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/4hu4 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/4hu4 | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 32861.820 Da / Num. of mol.: 2 / Fragment: EAL domain, UNP residues 529-799 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1489, dos, dosP, JW1484, yddU / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P76129, cyclic-guanylate-specific phosphodiesterase #2: 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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20 % PEG 6000, 0.2 M calcium chloride, 0.1 M HEPES pH 7.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97936 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2005 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.48 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 28963 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 94.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→19.992 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.48 / Phase error: 27.52 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.08 Å2 / Biso mean: 35.8263 Å2 / Biso min: 7.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→19.992 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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