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- PDB-2yq8: Crystal structure of the SeMet-labeled N-terminal domain and pept... -
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Open data
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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. | ||||||
![]() | PROLYL 4-HYDROXYLASE SUBUNIT ALPHA-1 | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() 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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Anantharajan, J. / Koski, M.K. / Wierenga, R.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.7 KB | Display | ![]() |
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PDB format | ![]() | 78.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bt8C ![]() 4bt9C ![]() 4btaC ![]() 4btbC ![]() 2v5fS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: P13674, procollagen-proline 4-dioxygenase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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