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Yorodumi- PDB-1s7d: Crystal structure of refined tetragonal crystal of YodA from Esch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s7d | ||||||
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Title | Crystal structure of refined tetragonal crystal of YodA from Escherichia coli | ||||||
Components | Metal-binding Protein yodA | ||||||
Keywords | STRUCTURAL GENOMICS / hypothetical / x-ray crytsallography / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information cellular response to zinc ion starvation / intracellular zinc ion homeostasis / cadmium ion binding / cellular response to cadmium ion / cellular response to hydrogen peroxide / outer membrane-bounded periplasmic space / zinc ion binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of refined tetragonal crystal of YodA from Escherichia coli Authors: Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s7d.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s7d.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/1s7d ftp://data.pdbj.org/pub/pdb/validation_reports/s7/1s7d | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24795.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yodA / Production host: Escherichia coli (E. coli) / References: UniProt: P76344 | ||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.32 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M zinc acetate, 0.1M sodium carcodylate, 18% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 2002 / Details: Monochromator |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→44.69 Å / Num. all: 13410 / Num. obs: 13276 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.6 Å2 |
Reflection shell | Resolution: 2.17→2.21 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→19.45 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 164588.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.3569 Å2 / ksol: 0.392174 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.17→19.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.31 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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