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Yorodumi- PDB-6te3: Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Co... -
+Open data
-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 | |||||||||||||||
Components | Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 | |||||||||||||||
Keywords | TRANSFERASE / Collagen / lysyl hydroxylase / hydroxylysine / galactosyltransferase / glucosyltransferase | |||||||||||||||
Function / homology | Function and homology information 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 / trans-Golgi network / protein localization / 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 | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||||||||
Authors | Chiapparino, A. / De Giorgi, F. / Scietti, L. / Faravelli, S. / Roscioli, T. / Forneris, F. | |||||||||||||||
Funding support | Italy, 4items
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Citation | Journal: Int J Mol Sci / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6te3.cif.gz | 355.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6te3.ent.gz | 238.6 KB | Display | PDB format |
PDBx/mmJSON format | 6te3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/6te3 ftp://data.pdbj.org/pub/pdb/validation_reports/te/6te3 | HTTPS FTP |
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-Related structure data
Related structure data | 6tecC 6tesC 6teuC 6texC 6tezC 6fxmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Gene: PLOD3 / Plasmid: pUPE.106.08 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) References: UniProt: O60568, procollagen-lysine 5-dioxygenase, procollagen galactosyltransferase, procollagen glucosyltransferase |
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-Sugars , 2 types, 2 molecules
#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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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