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Yorodumi- PDB-6evo: Crystal structure the peptide-substrate-binding domain of human t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6evo | ||||||
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Title | Crystal structure the peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Arg-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: 1.55 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 | 6evo.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6evo.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 6evo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/6evo ftp://data.pdbj.org/pub/pdb/validation_reports/ev/6evo | 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: 831.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide, commercial. / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Chemical | #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: 2.72 Å3/Da / Density % sol: 54.73 % |
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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 PPGPRGPPG, 10 mM EDTA, 100 mM MOPS |
-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: 1.55→48 Å / Num. obs: 19323 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.02 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 2 / Num. unique obs: 157 / Rpim(I) all: 0.366 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.55→47.962 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→47.962 Å
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Refine LS restraints |
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LS refinement shell |
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