+Open data
-Basic information
Entry | Database: PDB / ID: 2w6b | ||||||
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Title | Crystal Structure of the Trimeric beta-PIX Coiled-Coil Domain | ||||||
Components | RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 7 | ||||||
Keywords | SIGNALING PROTEIN / PHOSPHOPROTEIN / GUANINE-NUCLEOTIDE RELEASING FACTOR / GIT / PAK / PIX / COOL / RAC1 / GIT1 / CDC42 / COOL-1 / ARHGEF7 / BETA-PIX / SH3 DOMAIN / COILED-COIL | ||||||
Function / homology | Function and homology information presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle ...presynaptic actin cytoskeleton organization / negative regulation of microtubule nucleation / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / G alpha (12/13) signalling events / RHOQ GTPase cycle / RAC1 GTPase cycle / RHOA GTPase cycle / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / gamma-tubulin binding / lamellipodium assembly / small GTPase-mediated signal transduction / mitotic spindle pole / Golgi organization / Rho protein signal transduction / GABA-ergic synapse / hematopoietic progenitor cell differentiation / ruffle / guanyl-nucleotide exchange factor activity / lamellipodium / cell cortex / growth cone / postsynapse / neuron projection / positive regulation of apoptotic process / focal adhesion / centrosome / neuronal cell body / protein kinase binding / protein-containing complex / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Schlenker, O. / Rittinger, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structures of Dimeric Git1 and Trimeric Beta-Pix and Implications for Git-Pix Complex Assembly. Authors: Schlenker, O. / Rittinger, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w6b.cif.gz | 22.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w6b.ent.gz | 13.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w6b_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
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Full document | 2w6b_full_validation.pdf.gz | 427.1 KB | Display | |
Data in XML | 2w6b_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 2w6b_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/2w6b ftp://data.pdbj.org/pub/pdb/validation_reports/w6/2w6b | HTTPS FTP |
-Related structure data
Related structure data | 2w6aC 2ba2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6651.386 Da / Num. of mol.: 1 / Fragment: COILED-COIL, RESIDUES 588-638 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O55043 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE CRYSTALLIZED PROTEIN INCLUDES ONLY THE COILED-COIL DOMAIN OF BETA-PIX AND AS A CLONING ARTIFACT ...THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62 % Description: RESIDUES 230 TO 278 OF CHAIN C OF PDB ID 2BA2 WERE USED FOR MR. SEQUENCE ASSIGNMENT WAS CONFIRMED USING ANOMALOUS DIFFERENCE MAPS TO VERIFY THE PRESENCE OF THE SELENIUM SITES. |
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Crystal grow | Details: 35% MPD, 0.24 M NON-DETERGENT SULPHOBETAINE 195 (NDSB-195) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9698 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9698 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→40 Å / Num. obs: 2079 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 21 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 22 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 14.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BA2 Resolution: 2.8→39.72 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / ESU R: 0.94 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICALLY RELEVANT MOLECULE IS ARRANGED AROUND A NON-CRYSTALLOGRAPHIC THREEFOLD AXIS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→39.72 Å
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