+Open data
-Basic information
Entry | Database: PDB / ID: 1oej | ||||||
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Title | YodA from Escherichia coli crystallised with no added ions | ||||||
Components | HYPOTHETICAL PROTEIN YODA | ||||||
Keywords | STRESS PROTEIN/LIPOCALIN / STRESS PROTEIN / LIPOCALIN / YODA / STRESS PROTEIN-LIPOCALIN complex | ||||||
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: 1.81 Å | ||||||
Authors | David, G. / Blondeau, K. / Renouard, M. / Penel, S. / Lewit-Bentley, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oej.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oej.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 1oej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/1oej ftp://data.pdbj.org/pub/pdb/validation_reports/oe/1oej | HTTPS FTP |
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-Related structure data
Related structure data | 1oeeSC 1oekC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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) ESCHERICHIA COLI (E. coli) / References: UniProt: P76344 |
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#2: Chemical | ChemComp-NI / |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43 % |
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Crystal grow | pH: 6.5 Details: 10 MG/ML PROTEIN, 30% PEG 10000, 100 MM SODIUM CACODYLATE, PH = 6.5 200 MM SODIUM ACETATE |
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: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.3 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→14.92 Å / Num. obs: 6027 / % possible obs: 74.5 % / Redundancy: 1.6 % / Biso Wilson estimate: 20.107 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.6 / % possible all: 69.7 |
Reflection | *PLUS Highest resolution: 1.81 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OEE Resolution: 1.81→36.76 Å / SU B: 4.702 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.189 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 6 RESIDUES AT THE N-TERMINUS ARE DISORDERED
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Displacement parameters | Biso mean: 27.508 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→36.76 Å
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Refinement | *PLUS Highest resolution: 1.8 Å / Rfactor Rfree: 0.252 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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