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Open data
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Basic information
Entry | Database: PDB / ID: 1oek | ||||||
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Title | YodA from Escherichia coli crystallised with zinc ions | ||||||
![]() | METAL-BINDING PROTEIN ZINT | ||||||
![]() | METAL BINDING PROTEIN / STRESS PROTEIN / LIPOCALIN / YODA | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | David, G. / Blondeau, K. / Renouard, M. / Penel, S. / Lewit-Bentley, A. | ||||||
![]() | ![]() Title: Yoda from Escherichia Coli is a Metal-Binding, Lipocalin-Like Protein Authors: David, G. / Blondeau, K. / Schiltz, M. / Penel, S. / Lewit-Bentley, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.2 KB | Display | ![]() |
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PDB format | ![]() | 37.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.3 KB | Display | ![]() |
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Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 22373.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE: MAIRLYKLAVALGVFIVSAPAFS THAT IS INCLUDED THE SWISPROT RECORD UPSTREAM OF THE SEQUENCE ...THE SEQUENCE: MAIRLYKLAV | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | pH: 6.5 Details: 10 MG/ML PROTEIN, 10% PEG 10000, 100 MM SODIUM CACODYLATE, PH = 6.5 200 MM ZINC SULPHATE, 10% GLYCEROL |
Crystal grow | *PLUS Method: other / Details: David, G., (2002) Acta Cryst., D58, 1243. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→55.05 Å / Num. obs: 14176 / % possible obs: 98.6 % / Redundancy: 16.2 % / Biso Wilson estimate: 53.38 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 14.2 % / % possible all: 92.1 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 10445 / Redundancy: 12 % / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 71.1 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE FIRST 8 RESIDUES AT THE N-TERMINUS ARE DISORDERED
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Displacement parameters | Biso mean: 67.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→55.05 Å
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Refinement | *PLUS Rfactor Rfree: 0.35 / Rfactor Rwork: 0.269 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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