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Yorodumi- PDB-6evn: Crystal structure of peptide-substrate-binding domain of human ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6evn | ||||||
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Title | Crystal structure of peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complex with Pro-Pro-Gly-Pro-Ala-Gly-Pro-Pro-Gly. | ||||||
Components |
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Keywords | HYDROLASE / tetratricopeptide repeat / collagen synthesis / prolyl 4-hydroxylase | ||||||
Function / homology | Function and homology information procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / electron transfer activity / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å | ||||||
Authors | Murthy, A.V. / Sulu, R. / Koski, M.K. / Wierenga, R.K. | ||||||
Funding support | Finland, 1items
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Citation | Journal: Protein Sci. / Year: 2018 Title: Structural enzymology binding studies of the peptide-substrate-binding domain of human collagen prolyl 4-hydroxylase (type-II): High affinity peptides have a PxGP sequence motif. Authors: Murthy, A.V. / Sulu, R. / Koski, M.K. / Tu, H. / Anantharajan, J. / Sah-Teli, S.K. / Myllyharju, J. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6evn.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6evn.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 6evn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/6evn ftp://data.pdbj.org/pub/pdb/validation_reports/ev/6evn | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 11920.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: P4HA2, UNQ290/PRO330 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS References: UniProt: O15460, procollagen-proline 4-dioxygenase | ||||
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#2: Protein/peptide | Mass: 745.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide, commercial / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Chemical | ChemComp-DMS / #5: 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: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 2.45 M ammonium sulphate, 10% DMSO, 5 mM PPGPAGPPG, 5% D-galactose, 100 mM MOPS, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 30, 2017 |
Radiation | Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→47.6 Å / Num. obs: 21768 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.48→1.51 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 166 / Rpim(I) all: 0.322 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.48→28.943 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→28.943 Å
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Refine LS restraints |
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LS refinement shell |
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