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- PDB-1r1z: The Crystal structure of the Carbohydrate recognition domain of t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r1z | ||||||
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Title | The Crystal structure of the Carbohydrate recognition domain of the glycoprotein sorting receptor p58/ERGIC-53 reveals a novel metal binding site and conformational changes associated with calcium ion binding | ||||||
![]() | ERGIC-53 protein | ||||||
![]() | SUGAR BINDING PROTEIN / beta-sheet / calcium-binding / lectin / mammalian / endoplasmic reticulum | ||||||
Function / homology | ![]() postsynaptic Golgi apparatus / RHOD GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RHOA GTPase cycle / Cargo concentration in the ER / positive regulation of organelle organization / COPII-mediated vesicle transport / endoplasmic reticulum organization / COPII-coated ER to Golgi transport vesicle ...postsynaptic Golgi apparatus / RHOD GTPase cycle / RHOG GTPase cycle / RAC2 GTPase cycle / RHOA GTPase cycle / Cargo concentration in the ER / positive regulation of organelle organization / COPII-mediated vesicle transport / endoplasmic reticulum organization / COPII-coated ER to Golgi transport vesicle / Golgi organization / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / protein transport / Golgi membrane / glutamatergic synapse / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Velloso, L.M. / Svensson, K. / Pettersson, R.F. / Lindqvist, Y. | ||||||
![]() | ![]() Title: The Crystal Structure of the Carbohydrate-recognition Domain of the Glycoprotein Sorting Receptor p58/ERGIC-53 Reveals an Unpredicted Metal-binding Site and Conformational Changes Associated ...Title: The Crystal Structure of the Carbohydrate-recognition Domain of the Glycoprotein Sorting Receptor p58/ERGIC-53 Reveals an Unpredicted Metal-binding Site and Conformational Changes Associated with Calcium Ion Binding. Authors: Velloso, L.M. / Svensson, K. / Pettersson, R.F. / Lindqvist, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.7 KB | Display | ![]() |
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PDB format | ![]() | 160.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gv9S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
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Components
#1: Protein | Mass: 29027.236 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.39 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG8000, Calcium Chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→10 Å / Num. all: 98470 / Num. obs: 42617 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.096 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6205 / Rsym value: 0.33 / % possible all: 95.7 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 42111 / % possible obs: 94.6 % / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS % possible obs: 95.3 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1gv9 Resolution: 2.4→10 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.516 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0.005 / σ(I): 0.005 / ESU R: 0.49 / ESU R Free: 0.259 / 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: 21.012 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1833 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement | *PLUS Rfactor Rfree: 0.241 / Rfactor Rwork: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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