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Yorodumi- PDB-3ult: Crystal structure of an ice-binding protein from the perennial ry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ult | ||||||
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Title | Crystal structure of an ice-binding protein from the perennial ryegrass, Lolium perenne | ||||||
Components | Ice recrystallization inhibition protein-like protein | ||||||
Keywords | ANTIFREEZE PROTEIN / beta-solenoid / beta-roll / ice-binding / antifreeze / ice / extracellular | ||||||
Function / homology | Function and homology information Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Serralysin-like metalloprotease, C-terminal / Leucine-rich repeat domain superfamily / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Lolium perenne (perennial ryegrass) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å | ||||||
Authors | Middleton, A.J. / Faucher, F. / Campbell, R.L. / Davies, P.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Antifreeze protein from freeze-tolerant grass has a beta-roll fold with an irregularly structured ice-binding site. Authors: Middleton, A.J. / Marshall, C.B. / Faucher, F. / Bar-Dolev, M. / Braslavsky, I. / Campbell, R.L. / Walker, V.K. / Davies, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ult.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ult.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ult.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ult ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ult | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13503.053 Da / Num. of mol.: 2 / Fragment: UNP residues 137-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lolium perenne (perennial ryegrass) / Gene: IRI3 / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-star(DE3) / References: UniProt: B5T007 #2: Chemical | #3: Chemical | ChemComp-EOH / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 45-50% Ethanol, 100 mM Phosphate-citrate, 0-5% PEG 1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.13, 1.55 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 14, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Number: 51177 / Rmerge(I) obs: 0.073 / D res high: 2.1 Å / Num. obs: 23468 / % possible obs: 87.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.4→20 Å / Num. obs: 45098 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 17.982 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.057 / Net I/σ(I): 16.83 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SIRAS |
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.4→19.423 Å / Occupancy max: 1 / Occupancy min: 0.01 / SU ML: 0.28 / σ(F): 2 / Phase error: 20 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.897 Å2 / ksol: 0.493 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.65 Å2 / Biso mean: 17.308 Å2 / Biso min: 6.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19.423 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16
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