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Yorodumi- PDB-2pm9: Crystal structure of yeast Sec13/31 vertex element of the COPII v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pm9 | ||||||
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Title | Crystal structure of yeast Sec13/31 vertex element of the COPII vesicular coat | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / beta propeller | ||||||
Function / homology | Function and homology information Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat ...Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear pore localization / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / mating projection tip / endoplasmic reticulum organization / nucleocytoplasmic transport / vacuolar membrane / positive regulation of TOR signaling / mRNA transport / endoplasmic reticulum exit site / nuclear pore / : / positive regulation of TORC1 signaling / cell periphery / intracellular protein transport / protein import into nucleus / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Goldberg, J. / Fath, S. / Mancias, J.D. / Bi, X. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Structure and Organization of Coat Proteins in the COPII Cage. Authors: Fath, S. / Mancias, J.D. / Bi, X. / Goldberg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pm9.cif.gz | 145.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pm9.ent.gz | 110.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/2pm9 ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pm9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly unit involves this structure of the Sec13/31 vertex element together with the Sec13/31 edge element. |
-Components
#1: Protein | Mass: 45651.285 Da / Num. of mol.: 1 / Fragment: residues 1-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: WEB1, SEC31 / Production host: Hi5 insect cells / References: UniProt: P38968 |
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#2: Protein | Mass: 33191.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC13, ANU3 / Production host: Hi5 insect cells / References: UniProt: Q04491 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.78 Å3/Da / Density % sol: 74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 8% PEG 3350, 0.1M tri-sodium citrate, 10mM manganese chloride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→40 Å / Num. all: 21760 / Num. obs: 20444 / % possible obs: 92.6 % / Observed criterion σ(F): -5 / Observed criterion σ(I): -5 / Redundancy: 2.7 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.084 / Χ2: 2.081 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1644 / Rsym value: 0.347 / Χ2: 1.289 / % possible all: 76.3 |
-Phasing
Phasing MR | Rfactor: 0.541 / Cor.coef. Fo:Fc: 0.202 / Cor.coef. Io to Ic: 0.219
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Phasing dm | FOM : 0.48 / FOM acentric: 0.48 / FOM centric: 0.46 / Reflection: 18996 / Reflection acentric: 17786 / Reflection centric: 1210 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: yeast Sec13 Resolution: 3.3→40 Å / FOM work R set: 0.753 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 28.752 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.585 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→40 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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Xplor file |
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