[English] 日本語
Yorodumi- PDB-1g2b: ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2b | ||||||
---|---|---|---|---|---|---|---|
Title | ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT N47-D48 | ||||||
Components | SPECTRIN ALPHA CHAIN | ||||||
Keywords | METAL BINDING PROTEIN / CAPPING PROTEIN / CALCIUM-BINDING / DUPLICATION / SH3 DOMAIN / CYTOSKELETON | ||||||
Function / homology | Function and homology information costamere / actin filament capping / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.12 Å | ||||||
Authors | Berisio, R. / Viguera, A.R. / Serrano, L. / Wilmanns, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Atomic resolution structure of a mutant of the spectrin SH3 domain. Authors: Berisio, R. / Viguera, A. / Serrano, L. / Wilmanns, M. #1: Journal: Biochemistry / Year: 1999 Title: Thermodynamic Analysis of alpha-spectrin SH3 and Two of Its Circular Permutants with Different Loop Lengths: Discerning the Reasons for Rapid Folding in Proteins Authors: Martinez, J.C. / Viguera, A.R. / Berisio, R. / Wilmanns, M. / Mateo, P.L. / Filimonov, V.V. / Serrano, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g2b.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g2b.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 1g2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2b ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2b | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7129.172 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Details: CIRCULAR PERMUTANT, CUT AT N47-D48, INS(M-D48), INS(SG-T4) Source: (gene. exp.) Gallus gallus (chicken) / Organ: BRAIN / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P07751 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.51 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Details: Viguera, A.R., (1996) Nature Struct. Biol., 3, 874. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.12→14 Å / Num. all: 24461 / Num. obs: 24461 / % possible obs: 93.4 % / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 1.12→1.2 Å / Rmerge(I) obs: 0.14 / % possible all: 91.2 |
Reflection | *PLUS Num. measured all: 102998 |
Reflection shell | *PLUS % possible obs: 91.2 % |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: AB INITIO / Resolution: 1.12→14 Å / Num. parameters: 634 / Num. restraintsaints: 742 / Cross valid method: R-FREE / Stereochemistry target values: ENGH AND HUBER
| ||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | ||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 442 / Occupancy sum non hydrogen: 664 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→14 Å
| ||||||||||||||||
Refine LS restraints |
| ||||||||||||||||
LS refinement shell | Resolution: 1.12→14 Å
| ||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS σ(F): 4 / % reflection Rfree: 5 % / Rfactor all: 0.148 / Rfactor obs: 0.136 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |