[English] 日本語
Yorodumi- PDB-5xf7: Crystal structure of human protein disulfide isomerase-like prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xf7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human protein disulfide isomerase-like protein of the testis | ||||||
Components | Protein disulfide-isomerase-like protein of the testis | ||||||
Keywords | CHAPERONE | ||||||
Function / homology | Function and homology information germ cell migration / protein disulfide isomerase activity / spermatid development / protein folding / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.381 Å | ||||||
Authors | Li, H. / Li, J. / Liu, Y. / Liang, H. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Crystal and solution structures of human protein-disulfide isomerase-like protein of the testis (PDILT) provide insight into its chaperone activity Authors: Li, H. / Yang, K. / Wang, W. / Niu, Y. / Li, J. / Dong, Y. / Liu, Y. / Wang, C.C. / Wang, L. / Liang, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xf7.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xf7.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/5xf7 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/5xf7 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 66344.344 Da / Num. of mol.: 1 / Fragment: UNP residues 21-584 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDILT / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N807 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.21 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 21% (w/v) PEG 3350 and 0.1 M succinic acid, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 24401 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rsym value: 0.066 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.38→2.42 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.716 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EKZ, 4NWY Resolution: 2.381→28.106 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.19 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.381→28.106 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|