+Open data
-Basic information
Entry | Database: PDB / ID: 4a4p | ||||||
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Title | crystal structure of the Sec7 domain from human cytohesin1 | ||||||
Components | CYTOHESIN1 | ||||||
Keywords | SIGNALING PROTEIN / ALL ALPHA / GUANINE-NUCLEOTIDE RELEASING FACTOR | ||||||
Function / homology | Function and homology information Intra-Golgi traffic / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / adherens junction / cytoplasmic side of plasma membrane / Golgi membrane ...Intra-Golgi traffic / establishment of epithelial cell polarity / regulation of ARF protein signal transduction / bicellular tight junction / regulation of cell adhesion / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / adherens junction / cytoplasmic side of plasma membrane / Golgi membrane / lipid binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zeeh, J.C. / Thompson, A.W. / Cherfils, J. / Biou, V. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Sec7 Domain from Human Cytohesin1 Authors: Zeeh, J.C. / Thompson, A.W. / Cherfils, J. / Biou, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a4p.cif.gz | 94.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a4p.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 4a4p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a4p_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 4a4p_full_validation.pdf.gz | 435.2 KB | Display | |
Data in XML | 4a4p_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 4a4p_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/4a4p ftp://data.pdbj.org/pub/pdb/validation_reports/a4/4a4p | HTTPS FTP |
-Related structure data
Related structure data | 1r8mS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.88756, 0.15305, -0.43452), Vector: |
-Components
#1: Protein | Mass: 22355.488 Da / Num. of mol.: 2 / Fragment: SEC7 DOMAIN, RESIDUES 63-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q15438 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 7 Details: PEG 3350 12%, AMMONIUM ACETATE 0.4M. GLYCEROL CRYO-PROTECTANT., pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 13, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→80.2 Å / Num. obs: 79470 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 26.48 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R8M Resolution: 2→32.03 Å / Cor.coef. Fo:Fc: 0.9435 / Cor.coef. Fo:Fc free: 0.9199 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 28.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.203 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.08 Å / Total num. of bins used: 13
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