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Yorodumi- PDB-6evm: Crystal structure of a Pro-9 complexed peptide-substrate-binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6evm | ||||||
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Title | Crystal structure of a Pro-9 complexed peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 | 6evm.cif.gz | 37.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6evm.ent.gz | 25 KB | Display | PDB format |
PDBx/mmJSON format | 6evm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/6evm ftp://data.pdbj.org/pub/pdb/validation_reports/ev/6evm | HTTPS FTP |
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-Related structure data
Related structure data | 6evlSC 6evnC 6evoC 6evpC 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
#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: 892.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide having 9 proline residues. / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-SO4 / |
#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: 53.88 % |
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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, 2.5 mM Pro-9, 4% hexenediol, 100 mM MOPS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Aug 11, 2016 / Details: HELIOS MX MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.9 Å / Num. obs: 8956 / % possible obs: 99.4 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.019 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 384 / Rpim(I) all: 0.21 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EVL Resolution: 2→39.875 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.875 Å
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Refine LS restraints |
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LS refinement shell |
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