+Open data
-Basic information
Entry | Database: PDB / ID: 2wbl | ||||||
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Title | Three-dimensional structure of a binary ROP-PRONE complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / MEMBRANE / PRENYLATION / METHYLATION / NUCLEOTIDE- BINDING / NUCLEOTIDE-BINDING / COMPLEX OF PRONE-GEF WITH ROP SUBSTRATE / LIPOPROTEIN / GTP-BINDING | ||||||
Function / homology | Function and homology information cortical cytoskeleton organization / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / actin filament organization / cell projection / regulation of actin cytoskeleton organization / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization ...cortical cytoskeleton organization / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / actin filament organization / cell projection / regulation of actin cytoskeleton organization / cell cortex / regulation of cell shape / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / intracellular membrane-bounded organelle / GTPase activity / GTP binding / protein kinase binding / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Thomas, C. / Fricke, I. / Weyand, M. / Berken, A. | ||||||
Citation | Journal: Biol.Chem. / Year: 2009 Title: 3D Structure of a Binary Rop-Prone Complex: The Final Intermediate for a Complete Set of Molecular Snapshots of the Ropgef Reaction. Authors: Thomas, C. / Fricke, I. / Weyand, M. / Berken, A. #1: Journal: Mol.Cell / Year: 2007 Title: Structural Evidence for a Common Intermediate in Small G Protein-Gef Reactions. Authors: Thomas, C. / Fricke, I. / Scrima, A. / Berken, A. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wbl.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wbl.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wbl ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wbl | HTTPS FTP |
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-Related structure data
Related structure data | 2ntyS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 41516.367 Da / Num. of mol.: 2 / Fragment: PRONE DOMAIN, RESIDUES 76-440 Source method: isolated from a genetically manipulated source Details: ROPGEF8 / Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Variant: COL-0 / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS-RIL / References: UniProt: Q9LV40 #2: Protein | Mass: 19873.781 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-180 Source method: isolated from a genetically manipulated source Details: ROP7 / Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Variant: LANDSBERG ERECTA / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CODONPLUS-RIL / References: UniProt: Q38903 Sequence details | SERINE 28 IS A GLYCINE IN THE LANDSBERG ERECTA VARIANT | |
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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97634 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97634 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 30632 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.82 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.82 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NTY Resolution: 2.9→49.41 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.882 / SU B: 35.825 / SU ML: 0.31 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→49.41 Å
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