+Open data
-Basic information
Entry | Database: PDB / ID: 2b7m | ||||||
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Title | Crystal Structure of the S. cerevisiae Exocyst Component Exo70p | ||||||
Components | Exocyst complex component EXO70 | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / exocyst / exocytosis / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis ...exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis / exocytosis / Rho protein signal transduction / transport vesicle / phosphatidylinositol-4,5-bisphosphate binding / small GTPase binding / protein transport / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å | ||||||
Authors | Hamburger, Z.A. / Hamburger, A.E. / West, A.P. / Weis, W.I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structure of the S.cerevisiae Exocyst Component Exo70p Authors: Hamburger, Z.A. / Hamburger, A.E. / West, A.P. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b7m.cif.gz | 374.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b7m.ent.gz | 324.5 KB | Display | PDB format |
PDBx/mmJSON format | 2b7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b7m_validation.pdf.gz | 480.2 KB | Display | wwPDB validaton report |
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Full document | 2b7m_full_validation.pdf.gz | 584.1 KB | Display | |
Data in XML | 2b7m_validation.xml.gz | 81.5 KB | Display | |
Data in CIF | 2b7m_validation.cif.gz | 109 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b7m ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b7m | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 65537.406 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: EXO70 / Plasmid: pProEx-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): RIL+ / References: UniProt: P19658 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.65 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 0.1 M MES pH 6.1, 20 % PEG 20000, 0.2 M magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97950, 0.97963, 0.9393 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 5, 2004 | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.5→20 Å / Num. all: 36080 / Num. obs: 36080 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.076 / Net I/σ(I): 12.6 | ||||||||||||
Reflection shell | Resolution: 3.5→3.62 Å / Redundancy: 3 % / Rsym value: 0.354 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.5→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4031626.48 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.2292 Å2 / ksol: 0.157954 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 129.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.62 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |