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Yorodumi- PDB-6q3p: Atomic resolution crystal structure of an AAB collagen heterotrimer -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q3p | ||||||
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Title | Atomic resolution crystal structure of an AAB collagen heterotrimer | ||||||
Components |
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Keywords | PROTEIN BINDING / Collagen 1 / Heterotrimer / Discoidin Domain Receptor / Von Willebrand Factor | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å | ||||||
Authors | Jalan, A.A. / Hartgerink, J.D. / Brear, P. / Leitinger, B. / Farndale, R.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2019 Title: Atomic resolution crystal structure of an AAB collagen heterotrimer Authors: Jalan, A.A. / Hartgerink, J.D. / Brear, P. / Leitinger, B. / Farndale, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q3p.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q3p.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 6q3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q3p_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 6q3p_full_validation.pdf.gz | 455.3 KB | Display | |
Data in XML | 6q3p_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 6q3p_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q3p ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein/peptide , 3 types, 3 molecules ABC
#1: Protein/peptide | Mass: 4385.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: Protein/peptide | Mass: 4411.846 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Protein/peptide | Mass: 4471.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 3 types, 303 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.38 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 19% PEG monomethyl ether 2K, 0.1M Tris-HCl, pH 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→27.341973967 Å / Num. obs: 47206 / % possible obs: 94.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 11.81 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.03→1.05 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2336 / CC1/2: 0.894 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: idealized 16 amino acid triple helix Resolution: 1.03→27.34 Å / SU ML: 0.1127 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.03→27.34 Å
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Refine LS restraints |
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LS refinement shell |
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