+Open data
-Basic information
Entry | Database: PDB / ID: 1gv9 | ||||||
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Title | p58/ERGIC-53 | ||||||
Components | P58/ERGIC-53 | ||||||
Keywords | CARBOHYDRATE BINDING / LECTIN | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.46 Å | ||||||
Authors | Velloso, L.M. / Svensson, K. / Schneider, G. / Pettersson, R.F. / Lindqvist, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of the Carbohydrate Recognition Domain of P58/Ergic-53, a Protein Involved in Glycoprotein Export from the Endoplasmic Reticulum. Authors: Velloso, L.M. / Svensson, K. / Schneider, G. / Pettersson, R.F. / Lindqvist, Y. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gv9.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gv9.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 1gv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/1gv9 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/1gv9 | 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: 28301.328 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN / Source method: isolated from a natural source / Source: (natural) RATTUS NORVEGICUS (Norway rat) / References: UniProt: Q62902 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.25 / Details: pH 7.25 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→25 Å / Num. obs: 44706 / % possible obs: 95.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.2 |
Reflection shell | *PLUS Highest resolution: 1.46 Å / Lowest resolution: 1.51 Å / % possible obs: 84.6 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 7.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.46→23.64 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.402 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→23.64 Å
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Refine LS restraints |
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