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Yorodumi- PDB-3bj5: Alternative conformations of the x region of human protein disulp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bj5 | ||||||
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Title | Alternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain | ||||||
Components | Protein disulfide-isomerase | ||||||
Keywords | ISOMERASE / Thioredoxin fold / Chaperone / Endoplasmic reticulum / Membrane / Redox-active center | ||||||
Function / homology | Function and homology information regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline ...regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / endoplasmic reticulum chaperone complex / Chylomicron assembly / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / positive regulation of cell adhesion / protein-disulfide reductase activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ruddock, L.W. / Nguyen, V.D. / Wierenga, R.K. / Haapalainen, A.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Alternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain Authors: Nguyen, V.D. / Wallis, K. / Howard, M.J. / Haapalainen, A.M. / Salo, K.E.H. / Saaranen, M.J. / Sidhu, A. / Wierenga, R.K. / Freedman, R.B. / Ruddock, L.W. / Williamson, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bj5.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bj5.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bj5 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bj5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17270.775 Da / Num. of mol.: 1 / Fragment: b'x domain, UNPR residues 230-368 / Mutation: I272A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Plasmid: pet23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P07237, protein disulfide-isomerase |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 1.88 Å3/Da / Density % sol: 34.54 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.95M Ammonium sulfate, 0.2M NaCl, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.89997 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2006 |
Radiation | Monochromator: Double crystal Si[111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89997 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.69 Å / Num. all: 6879 / Num. obs: 6879 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 41.042 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.84 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 17.8 / Num. unique all: 849 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→18.11 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.505 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.401 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→18.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.474 Å / Origin y: 3.673 Å / Origin z: 5.687 Å
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