+Open data
-Basic information
Entry | Database: PDB / ID: 3ahq | ||||||
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Title | hyperactive human Ero1 | ||||||
Components | ERO1-like protein alpha | ||||||
Keywords | OXIDOREDUCTASE / disulfide bond / PDI / redox / hyperactive human Ero1 | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / thiol oxidase activity / protein folding in endoplasmic reticulum / protein maturation by protein folding / response to temperature stimulus / Detoxification of Reactive Oxygen Species / chaperone cofactor-dependent protein refolding / protein-disulfide reductase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / brown fat cell differentiation ...Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / thiol oxidase activity / protein folding in endoplasmic reticulum / protein maturation by protein folding / response to temperature stimulus / Detoxification of Reactive Oxygen Species / chaperone cofactor-dependent protein refolding / protein-disulfide reductase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / brown fat cell differentiation / endoplasmic reticulum unfolded protein response / release of sequestered calcium ion into cytosol / FAD binding / response to endoplasmic reticulum stress / extracellular matrix organization / cell redox homeostasis / protein modification process / Golgi lumen / protein folding / cellular response to hypoxia / response to oxidative stress / oxidoreductase activity / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / dendrite / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Inaba, K. / Sitia, R. / Suzuki, M. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Crystal structures of human Ero1-alpha reveal the mechanisms of regulated and targeted oxidation of PDI Authors: Inaba, K. / Masui, S. / Iida, H. / Vavassori, S. / Sitia, R. / Suzuki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ahq.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ahq.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ahq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/3ahq ftp://data.pdbj.org/pub/pdb/validation_reports/ah/3ahq | HTTPS FTP |
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-Related structure data
Related structure data | 3ahrC 1rp4S 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: 54172.832 Da / Num. of mol.: 1 / Mutation: C104A, C131A, C166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Ero1-Lalpha / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q96HE7, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor |
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#2: Chemical | ChemComp-FAD / |
#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: 2.59 Å3/Da / Density % sol: 52.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 8% PEG4000, 50mM imidazole pH8.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 4, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→41.5 Å / Num. obs: 23814 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.054 / Rsym value: 0.058 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.35→2.47 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.473 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDN ENTRY 1RP4 Resolution: 2.35→36.27 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.799 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.25 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.619 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→36.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.347→2.408 Å / Total num. of bins used: 20
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