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Yorodumi- PDB-4zvb: Crystal structure of globin domain of the E. coli DosC - form II ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zvb | ||||||
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Title | Crystal structure of globin domain of the E. coli DosC - form II (ferrous) | ||||||
Components | Diguanylate cyclase DosC | ||||||
Keywords | SIGNALING PROTEIN / oxygen sensing / diguanylate cyclase / cyclic-di-GMP / transferase | ||||||
Function / homology | Function and homology information negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / oxygen binding / heme binding / GTP binding / protein homodimerization activity ...negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / carbon monoxide binding / response to oxygen levels / cell adhesion involved in single-species biofilm formation / oxygen binding / heme binding / GTP binding / protein homodimerization activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Tarnawski, M. / Barends, T.R.M. / Schlichting, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural analysis of an oxygen-regulated diguanylate cyclase. Authors: Tarnawski, M. / Barends, T.R. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zvb.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zvb.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 4zvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zvb ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zvb | HTTPS FTP |
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-Related structure data
Related structure data | 4zvaSC 4zvcC 4zvdC 4zveC 4zvfC 4zvgC 4zvhC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19115.004 Da / Num. of mol.: 4 / Fragment: UNP residues 1-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: dosC, yddV, b1490, JW5241 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA89, diguanylate cyclase #2: Chemical | ChemComp-HEM / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M sodium phosphate-citrate pH 4.2, 0.2 M sodium chloride, 16% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.7345 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7345 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 22142 / % possible obs: 94.6 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.36 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.64 / % possible all: 88.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZVA Resolution: 2.4→45.341 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.1 / 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: 2.4→45.341 Å
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Refine LS restraints |
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LS refinement shell |
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