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Yorodumi- PDB-4i6x: Crystal Structure of Non-catalyic Domain of Protein Disulfide Iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i6x | ||||||
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Title | Crystal Structure of Non-catalyic Domain of Protein Disulfide Isomerase-related (PDIr) Protein | ||||||
Components | Protein disulfide-isomerase A5 | ||||||
Keywords | ISOMERASE / thioredoxin-like fold / protein binding / endoplasmic reticulum | ||||||
Function / homology | Function and homology information protein-disulfide reductase activity => GO:0015035 / protein disulfide-isomerase / : / XBP1(S) activates chaperone genes / protein disulfide isomerase activity / IRE1-mediated unfolded protein response / cell redox homeostasis / protein folding / oxidoreductase activity / endoplasmic reticulum lumen / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Kozlov, G. / Vinaik, R. / Gehring, K. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Structure of the Non-Catalytic Domain of the Protein Disulfide Isomerase-Related Protein (PDIR) Reveals Function in Protein Binding. Authors: Vinaik, R. / Kozlov, G. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i6x.cif.gz | 58.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i6x.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 4i6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6x ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6x | 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: 15024.337 Da / Num. of mol.: 1 / Fragment: non-catalytic domain (UNP residues 29-150) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA5, PDIR / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q14554, protein disulfide-isomerase |
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#2: 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: 2.16 Å3/Da / Density % sol: 43.18 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.15 M DL-malic acid, 20% PEG3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 20332 / Num. obs: 19332 / % possible obs: 95.08 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rsym value: 0.031 / Net I/σ(I): 43.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 972 / Rsym value: 0.268 / % possible all: 67.01 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→45.45 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.367 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.079 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.386 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→45.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.543 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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