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Yorodumi- PDB-4gmv: Crystal Structure of the coiled-coil, RA and PH domains of Lamell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gmv | ||||||
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Title | Crystal Structure of the coiled-coil, RA and PH domains of Lamellipodin | ||||||
Components | Ras-associated and pleckstrin homology domains-containing protein 1 | ||||||
Keywords | CELL ADHESION / RA-PH / coiled-coil region / Ras-association domain / pleckstrin homology domain / cytoskeletal protein / Ena/VASP binding / cell migration | ||||||
Function / homology | Function and homology information axon extension / filopodium / lamellipodium / cytoskeleton / nuclear body / signal transduction / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å | ||||||
Authors | Chang, Y.C.E. / Wu, J. | ||||||
Citation | Journal: Protein Cell / Year: 2013 Title: Crystal structure of Lamellipodin implicates diverse functions in actin polymerization and Ras signaling. Authors: Chang, Y.C. / Zhang, H. / Brennan, M.L. / Wu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gmv.cif.gz | 229.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gmv.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 4gmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/4gmv ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gmv | HTTPS FTP |
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-Related structure data
Related structure data | 4gn1C 3tcaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33234.422 Da / Num. of mol.: 2 / Fragment: coiled-coil, RA, PH domain (UNP Residues 240-520) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAPH1, ALS2CR18, ALS2CR9, KIAA1681, LPD, PREL2, RMO1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q70E73 #2: 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: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50 mM sodium formate, 20% (w/v) polyethylene glycol 3350, 30% (v/v) ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2012 |
Radiation | Monochromator: Bent single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38 Å / Num. obs: 24426 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TCA Resolution: 2.403→37.96 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.894 / SU B: 19.118 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 50.181 Å2
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Refinement step | Cycle: LAST / Resolution: 2.403→37.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.403→2.465 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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