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Yorodumi- PDB-1ezg: CRYSTAL STRUCTURE OF ANTIFREEZE PROTEIN FROM THE BEETLE, TENEBRIO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ezg | ||||||
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Title | CRYSTAL STRUCTURE OF ANTIFREEZE PROTEIN FROM THE BEETLE, TENEBRIO MOLITOR | ||||||
Components | THERMAL HYSTERESIS PROTEIN ISOFORM YL-1Antifreeze protein | ||||||
Keywords | ANTIFREEZE PROTEIN / insect antifreeze protein / thermal hysteresis / Tenebrio molitor / iodination / right-handed beta-helix / TmAFP | ||||||
Function / homology | Insect antifreeze protein / Insect antifreeze protein motif / Insect cysteine-rich antifreeze protein / Insect antifreeze protein repeat / Pectate Lyase C-like / 3 Solenoid / extracellular region / Mainly Beta / Thermal hysteresis protein YL-1 Function and homology information | ||||||
Biological species | Tenebrio molitor (yellow mealworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å | ||||||
Authors | Liou, Y.-C. / Tocilj, A. / Davies, P.L. / Jia, Z. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Mimicry of ice structure by surface hydroxyls and water of a beta-helix antifreeze protein. Authors: Liou, Y.C. / Tocilj, A. / Davies, P.L. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ezg.cif.gz | 33 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ezg.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ezg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/1ezg ftp://data.pdbj.org/pub/pdb/validation_reports/ez/1ezg | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | In solution, it is monomer. But it is a dimer in crystal. |
-Components
#1: Protein | Mass: 8389.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tenebrio molitor (yellow mealworm) / Description: LARVAE HEMOLYMPH / Gene: CDNA FROM FAT BODY LIBRARY / Plasmid: PET20B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O16119 |
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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: 2.49 Å3/Da / Density % sol: 50.62 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, sodium citra, cobalt chloridee, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.91 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→25 Å / Num. all: 133370 / Num. obs: 32557 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.208 / Num. unique all: 3086 / % possible all: 95.6 |
Reflection shell | *PLUS % possible obs: 95.6 % |
-Processing
Software |
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Refinement | Resolution: 1.4→5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.4→5 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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