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Yorodumi- PDB-4z1r: Crystal structure of collagen-like peptide at 1.27 Angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z1r | ||||||
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Title | Crystal structure of collagen-like peptide at 1.27 Angstrom resolution | ||||||
Components | Collagen-like peptide | ||||||
Keywords | STRUCTURAL PROTEIN / Collagen / triple helix | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Plonska-Brzezinska, M.E. / Czyrko, J. / Brus, D.M. / Imierska, M. / Brzezinski, K. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Rsc Adv / Year: 2015 Title: Triple helical collagen-like peptide interactions with selected polyphenolic compounds. Authors: Plonska-Brzezinska, M.E. / Bobrowska, D.M. / Sharma, A. / Rodziewicz, P. / Tomczyk, M. / Czyrko, J. / Brzezinski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z1r.cif.gz | 42.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z1r.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 4z1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/4z1r ftp://data.pdbj.org/pub/pdb/validation_reports/z1/4z1r | HTTPS FTP |
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-Related structure data
Related structure data | 1cagS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m34z1r / Data set type: diffraction image data |
Experimental dataset #2 | Data reference: 10.18430/m34z1r / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2704.854 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Water | ChemComp-HOH / | |
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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: 1.83 Å3/Da / Density % sol: 32.96 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 400, 5% acetic acid |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 13, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 60616 / Rmerge(I) obs: 0.052 / Χ2: 0.96 / D res high: 1.27 Å / Num. obs: 16057 / % possible obs: 98.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.27→30 Å / Num. obs: 16057 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 11.523 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.06 / Χ2: 0.962 / Net I/σ(I): 17.15 / Num. measured all: 60616 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CAG Resolution: 1.27→28.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.402 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 37.07 Å2 / Biso mean: 8.171 Å2 / Biso min: 2.92 Å2
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Refinement step | Cycle: final / Resolution: 1.27→28.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.269→1.302 Å / Total num. of bins used: 20
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