+Open data
-Basic information
Entry | Database: PDB / ID: 4gky | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a carbohydrate-binding domain | ||||||
Components | Protein ERGIC-53 | ||||||
Keywords | PROTEIN TRANSPORT / Endoplasmic reticulum | ||||||
Function / homology | Function and homology information Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / endoplasmic reticulum organization / RHOD GTPase cycle / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / ER to Golgi transport vesicle membrane / blood coagulation / unfolded protein binding / protein transport / protein folding / collagen-containing extracellular matrix / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular exosome / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4201 Å | ||||||
Authors | Page, R.C. / Zheng, C. / Nix, J.C. / Misra, S. / Zhang, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural Characterization of Carbohydrate Binding by LMAN1 Protein Provides New Insight into the Endoplasmic Reticulum Export of Factors V (FV) and VIII (FVIII). Authors: Zheng, C. / Page, R.C. / Das, V. / Nix, J.C. / Wigren, E. / Misra, S. / Zhang, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4gky.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4gky.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/4gky ftp://data.pdbj.org/pub/pdb/validation_reports/gk/4gky | HTTPS FTP |
---|
-Related structure data
Related structure data | 4gkxC 3a4uS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28672.803 Da / Num. of mol.: 1 Fragment: Carbohydrate Recognition Domain UNP Residues 31-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERGIC53, F5F8D, LMAN1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P49257 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Sugar | ChemComp-MAN / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.57 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 17% PEG 8000, 0.002M calcium chloride, 0.01M alpha-1,2-dimannose, 0.05M sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2011 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→47.75 Å / Num. all: 10429 / Num. obs: 10429 / % possible obs: 100 % / Observed criterion σ(F): 23 / Observed criterion σ(I): 23 |
Reflection shell | Resolution: 2.42→2.55 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 7.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A4U Resolution: 2.4201→38.332 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 21.23 / 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: 2.4201→38.332 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|