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Open data
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Basic information
Entry | Database: PDB / ID: 2wbl | ||||||
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Title | Three-dimensional structure of a binary ROP-PRONE complex | ||||||
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![]() | SIGNALING PROTEIN / MEMBRANE / PRENYLATION / METHYLATION / NUCLEOTIDE- BINDING / NUCLEOTIDE-BINDING / COMPLEX OF PRONE-GEF WITH ROP SUBSTRATE / LIPOPROTEIN / GTP-BINDING | ||||||
Function / homology | ![]() cortical cytoskeleton organization / small GTPase-mediated signal transduction / guanyl-nucleotide exchange factor activity / cell projection / regulation of actin cytoskeleton organization / actin filament 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 / cell projection / regulation of actin cytoskeleton organization / actin filament 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomas, C. / Fricke, I. / Weyand, M. / Berken, A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.7 KB | Display | ![]() |
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PDB format | ![]() | 152.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.6 KB | Display | ![]() |
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Full document | ![]() | 472.2 KB | Display | |
Data in XML | ![]() | 34.1 KB | Display | |
Data in CIF | ![]() | 47 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ntyS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() Sequence details | SERINE 28 IS A GLYCINE IN THE LANDSBERG ERECTA VARIANT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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Refine LS restraints |
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