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- PDB-6te3: Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6te3 | |||||||||||||||
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Title | Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Cocrystal with Fe2+, Mn2+, UDP | |||||||||||||||
![]() | Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 | |||||||||||||||
![]() | TRANSFERASE / Collagen / lysyl hydroxylase / hydroxylysine / galactosyltransferase / glucosyltransferase | |||||||||||||||
Function / homology | ![]() procollagen galactosyltransferase / procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen galactosyltransferase activity / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / basement membrane assembly / epidermis morphogenesis ...procollagen galactosyltransferase / procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen galactosyltransferase activity / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / basement membrane assembly / epidermis morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / endothelial cell morphogenesis / protein O-linked glycosylation / L-ascorbic acid binding / collagen fibril organization / neural tube development / lung morphogenesis / small molecule binding / rough endoplasmic reticulum / protein localization / trans-Golgi network / vasodilation / collagen-containing extracellular matrix / in utero embryonic development / iron ion binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / metal ion binding 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 | ![]() | 355.2 KB | Display | ![]() |
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PDB format | ![]() | 238.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tecC ![]() 6tesC ![]() 6teuC ![]() 6texC ![]() 6tezC ![]() 6fxmS 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: 82784.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: O60568, procollagen-lysine 5-dioxygenase, procollagen galactosyltransferase, procollagen glucosyltransferase |
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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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#7: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 162 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-AKG / | #5: Chemical | #6: Chemical | ChemComp-MN / | #8: 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: 3.31 Å3/Da / Density % sol: 62.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.8 Details: 600 mM sodium formate, 12% PGA-LM, 100 mM HEPES/NaOH, 500 mM FeCl2, 500 mM MnCl2, 1 mM UDP 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 4M / Detector: PIXEL / Date: Apr 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.84 Å / Num. obs: 48288 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 26.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.086 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.476 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4455 / CC1/2: 0.512 / Rpim(I) all: 1.107 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FXM Resolution: 2.3→48.84 Å / SU ML: 0.2684 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0174
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.84 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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