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Yorodumi- PDB-2yq8: Crystal structure of the SeMet-labeled N-terminal domain and pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yq8 | ||||||
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Title | Crystal structure of the SeMet-labeled N-terminal domain and peptide substrate binding domain of alpha subunit of prolyl-4 hydroxylase type I from human. | ||||||
Components | PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase complex / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / collagen fibril organization / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum ...procollagen-proline 4-dioxygenase / procollagen-proline 4-dioxygenase complex / procollagen-proline 4-dioxygenase activity / Collagen biosynthesis and modifying enzymes / L-ascorbic acid binding / collagen fibril organization / iron ion binding / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum / mitochondrion / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.987 Å | ||||||
Authors | Anantharajan, J. / Koski, M.K. / Wierenga, R.K. | ||||||
Citation | Journal: Structure / Year: 2013 Title: The Structural Motifs for Substrate Binding and Dimerization of the Alpha Subunit of Collagen Prolyl 4-Hydroxylase Authors: Anantharajan, J. / Koski, M.K. / Kursula, P. / Hieta, R. / Bergmann, U. / 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 | 2yq8.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yq8.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 2yq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yq8_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 2yq8_full_validation.pdf.gz | 443.4 KB | Display | |
Data in XML | 2yq8_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2yq8_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/2yq8 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/2yq8 | HTTPS FTP |
-Related structure data
Related structure data | 4bt8C 4bt9C 4btaC 4btbC 2v5fS 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
#1: Protein | Mass: 27800.457 Da / Num. of mol.: 2 / Fragment: COLLAGEN BINDING DOMAIN, RESIDUES 18-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 References: UniProt: P13674, procollagen-proline 4-dioxygenase #2: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 26-29% PEGMME 2000, 200MM KSCN AND 5MM DTT, 5MM SPERMINE TETRAHYDROCHLORIDE, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9737 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9737 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→45 Å / Num. obs: 19064 / % possible obs: 96.7 % / Observed criterion σ(I): 2.9 / Redundancy: 3.4 % / Biso Wilson estimate: 52.28 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.23 |
Reflection shell | Resolution: 2.99→3.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 73.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V5F Resolution: 2.987→44.622 Å / SU ML: 0.43 / σ(F): 1.37 / Phase error: 30.37 / Stereochemistry target values: ML Details: RESIDUES 1-6, 138-143, 238 IN CHAIN A & RESIDUES 1-6, 138-142, 238 IN CHAIN B ARE DISORDERED.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.987→44.622 Å
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Refine LS restraints |
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LS refinement shell |
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