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Yorodumi- PDB-1j72: Crystal Structure of Mutant Macrophage Capping Protein (Cap G) wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j72 | ||||||
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Title | Crystal Structure of Mutant Macrophage Capping Protein (Cap G) with Actin-severing Activity in the Ca2+-Free Form | ||||||
Components | Macrophage capping protein | ||||||
Keywords | STRUCTURAL PROTEIN / actin / human / capping / cap g / macrophage / gCap39 / Mbhl / gelsolin | ||||||
Function / homology | Function and homology information F-actin capping protein complex / actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / Flemming body / ruffle / phosphatidylinositol-4,5-bisphosphate binding / centriole / central nervous system development ...F-actin capping protein complex / actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / cell projection assembly / Flemming body / ruffle / phosphatidylinositol-4,5-bisphosphate binding / centriole / central nervous system development / mitotic spindle / actin filament binding / melanosome / actin cytoskeleton / lamellipodium / protein-containing complex assembly / cadherin binding / protein domain specific binding / protein-containing complex binding / nucleolus / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Vorobiev, S.M. / Southwick, F.S. / Storokopytov, B. / Almo, S.C. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Mutant Human Macrophage Capping Protein Authors: Vorobiev, S.M. / Southwick, F.S. / Storokopytov, B. / Almo, S.C. #1: Journal: J.Biol.Chem. / Year: 1995 Title: Gain-of-function mutations conferring actin-severing activity to human macrophage Cap G Authors: Southwick, F.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j72.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j72.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 1j72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j72 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j72 | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 38625.477 Da / Num. of mol.: 1 Mutation: 108HLNTLLGE -> 108QLDDYLGG; 148AFHTSTGAPAAIKK -> 148GFKHVVPNEVVVQR Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40121 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.48 Å3/Da / Density % sol: 72.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M Tris-HCl, pH 7.0-8.0, 3.5 - 4.0 ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97178 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97178 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. all: 24873 / Num. obs: 24873 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.86 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 2.5→2.53 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.431 / Num. unique all: 1051 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→14.96 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2189205.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.11 Å2 / ksol: 0.308 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→14.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
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