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- PDB-6tex: Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Va... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tex | |||||||||||||||
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Title | Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucose | |||||||||||||||
![]() | Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 | |||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Chiapparino, A. / De Giorgi, F. / Scietti, L. / Faravelli, S. / Roscioli, T. / Forneris, F. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Identification of Regulatory Molecular 'Hot Spots' for LH/PLOD Collagen Glycosyltransferase Activity Authors: Mattoteia, D. / Chiapparino, A. / Fumagalli, M. / De Marco, M. / De Giorgi, F. / Negro, L. / Pinnola, A. / Faravelli, S. / Roscioli, T. / Scietti, L. / Forneris, F. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 367.1 KB | Display | ![]() |
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PDB format | ![]() | 247.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6te3C ![]() 6tecC ![]() 6tesC ![]() 6teuC ![]() 6tezC ![]() 6fxkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 82814.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Val80Lys Mutation - First Ser residue and last three Ala residues were introduced by molecular cloning Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O60568, ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source |
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#8: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 6 types, 117 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ChemComp-AKG / | ![]() #5: Chemical | ChemComp-UDP / | ![]() #6: Chemical | #7: Chemical | ChemComp-MN / | #9: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.24 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 600 mM sodium formate, 12% PGA-LM, 100 mM HEPES/NaOH, 500 uM FeCl2, 500 uM MnCl2, 1 mM UDP-Glucose Temp details: cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→49.02 Å / Num. obs: 49068 / % possible obs: 98.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 38.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.071 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 1.351 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4243 / CC1/2: 0.461 / Rpim(I) all: 1.155 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6FXK Resolution: 2.3→49 Å / SU ML: 0.3122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.529
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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