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Yorodumi- PDB-3h1q: Crystal structure of ethanolamine utilization protein EutJ from C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h1q | ||||||
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Title | Crystal structure of ethanolamine utilization protein EutJ from Carboxydothermus hydrogenoformans | ||||||
Components | Ethanolamine utilization protein EutJ | ||||||
Keywords | STRUCTURAL PROTEIN / Carboxydothermus hydrogenoformans / ethanolamine utilization protein EutJ / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Carboxydothermus hydrogenoformans Z-2901 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Chang, C. / Tesar, C. / Jedrzejczak, R. / Kinney, J. / Kerfeld, C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of ethanolamine utilization protein EutJ from Carboxydothermus hydrogenoformans Authors: Chang, C. / Tesar, C. / Jedrzejczak, R. / Kinney, J. / Kerfeld, C. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h1q.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h1q.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/3h1q ftp://data.pdbj.org/pub/pdb/validation_reports/h1/3h1q | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29106.287 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carboxydothermus hydrogenoformans Z-2901 (bacteria) Strain: Z-2901 / DSM 6008 / Gene: eutJ, CHY_0686 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3AE93 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THERE IS ARG AT SEQUENCE POSITION 201 ACCORDING TO ELECTRON DENSITY. | |
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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: 3.75 Å3/Da / Density % sol: 67.22 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6 M Magnesium sulfate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937, 0.97951 | |||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2009 | |||||||||
Radiation | Monochromator: Si(111) double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→50 Å / Num. all: 22341 / Num. obs: 22341 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 69.5 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 51.5 | |||||||||
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 7.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.896 / SU B: 32.919 / SU ML: 0.293 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.569 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROGRAM CNS HAS ALSO BEEN USED IN REFINEMENT.
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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: 44.578 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.88 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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