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Yorodumi- PDB-3eea: The crystal structure of the GAF domain/HD domain protein from Ge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eea | ||||||
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Title | The crystal structure of the GAF domain/HD domain protein from Geobacter sulfurreducens | ||||||
Components | GAF domain/HD domain protein | ||||||
Keywords | structural genomics / unknown function / GAF domain/HD domain protein / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacter sulfurreducens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of the GAF domain/HD domain protein from Geobacter sulfurreducens Authors: Zhang, R. / Hatzos, C. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eea.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eea.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 3eea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/3eea ftp://data.pdbj.org/pub/pdb/validation_reports/ee/3eea | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This protein may exists as dimer. |
-Components
#1: Protein | Mass: 18434.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: PCA / Gene: GSU1007 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q74EF5 #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: 2.15 Å3/Da / Density % sol: 42.84 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M CaCl2, 0.1M Tris, 20%(w/v)PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 21, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→64.96 Å / Num. all: 28838 / Num. obs: 28282 / % possible obs: 98.07 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 24.57 |
Reflection shell | Resolution: 1.8→1.847 Å / Redundancy: 3 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 1.12 / Num. unique all: 2228 / % possible all: 90.48 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→64.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.921 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.138 / ESU R Free: 0.134 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.627 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→64.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -7.268 Å / Origin y: -3.461 Å / Origin z: 11.635 Å
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Refinement TLS group |
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