+Open data
-Basic information
Entry | Database: PDB / ID: 3t9o | ||||||
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Title | Regulatory CZB domain of DgcZ | ||||||
Components | Diguanylate cyclase DgcZ | ||||||
Keywords | METAL BINDING PROTEIN / diguanylate cyclase / putative zinc sensor / CZB domain | ||||||
Function / homology | Function and homology information negative regulation of bacterial-type flagellum assembly / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of single-species biofilm formation on inanimate substrate / diguanylate cyclase / diguanylate cyclase activity / cell pole / cell adhesion involved in single-species biofilm formation / metabolic process / GTP binding / protein homodimerization activity ...negative regulation of bacterial-type flagellum assembly / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of single-species biofilm formation on inanimate substrate / diguanylate cyclase / diguanylate cyclase activity / cell pole / cell adhesion involved in single-species biofilm formation / metabolic process / GTP binding / protein homodimerization activity / zinc ion binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Zaehringer, F. / Schirmer, T. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structure and signaling mechanism of a zinc-sensory diguanylate cyclase. Authors: Zahringer, F. / Lacanna, E. / Jenal, U. / Schirmer, T. / Boehm, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t9o.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t9o.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 3t9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/3t9o ftp://data.pdbj.org/pub/pdb/validation_reports/t9/3t9o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | dimer |
-Components
#1: Protein | Mass: 15715.771 Da / Num. of mol.: 2 / Fragment: unp residues 2-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1535, JW1528, ydeG, ydeH / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P31129, diguanylate cyclase #2: Chemical | #3: 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: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 200mM ammonium tartrate, 12.5% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 27377 / Num. obs: 27196 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 38.08 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 10.72 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.71 / Num. unique all: 2049 / Rsym value: 0.382 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 0 / SU B: 12.787 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.47 Å2 / Biso mean: 33.469 Å2 / Biso min: 16.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 24.4987 Å / Origin y: 37.0022 Å / Origin z: 8.5617 Å
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Refinement TLS group |
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