+Open data
-Basic information
Entry | Database: PDB / ID: 3idv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the a0a fragment of ERp72 | ||||||
Components | Protein disulfide-isomerase A4 | ||||||
Keywords | ISOMERASE / thioredoxin-like fold / Disulfide bond / Endoplasmic reticulum / Redox-active center | ||||||
Function / homology | Function and homology information protein-disulfide reductase activity => GO:0015035 / protein disulfide-isomerase / protein disulfide isomerase activity / protein secretion / chaperone-mediated protein folding / response to endoplasmic reticulum stress / cell redox homeostasis / melanosome / protein folding / endoplasmic reticulum lumen ...protein-disulfide reductase activity => GO:0015035 / protein disulfide-isomerase / protein disulfide isomerase activity / protein secretion / chaperone-mediated protein folding / response to endoplasmic reticulum stress / cell redox homeostasis / melanosome / protein folding / endoplasmic reticulum lumen / cell surface / endoplasmic reticulum / extracellular space / RNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Kozlov, G. / Gehring, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Structure of the Catalytic a(0)a Fragment of the Protein Disulfide Isomerase ERp72. Authors: Kozlov, G. / Azeroual, S. / Rosenauer, A. / Maattanen, P. / Denisov, A.Y. / Thomas, D.Y. / Gehring, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3idv.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3idv.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 3idv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3idv ftp://data.pdbj.org/pub/pdb/validation_reports/id/3idv | HTTPS FTP |
---|
-Related structure data
Related structure data | 2b5eS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26837.305 Da / Num. of mol.: 1 / Fragment: a0a catalytic domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA4, ERP70, ERP72 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P13667, protein disulfide-isomerase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.01M zinc chloride, 20% PEG 6000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9995 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2007 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9995 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 18326 / Num. obs: 18308 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1284 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2b5e Resolution: 1.95→45.83 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.057 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.472 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→45.83 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.954→2.004 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|