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- PDB-1tuc: ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT ... -

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Basic information

Entry
Database: PDB / ID: 1tuc
TitleALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT S19-P20
ComponentsALPHA-SPECTRIN
KeywordsCYTOSKELETON / CAPPING PROTEIN / CALCIUM-BINDING / DUPLICATION / SH3 DOMAIN
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
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / SH3 type barrels. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.02 Å
AuthorsWilmanns, M. / Serrano, L. / Viguera, A.R.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics.
Authors: Viguera, A.R. / Blanco, F.J. / Serrano, L.
History
DepositionFeb 29, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-SPECTRIN


Theoretical massNumber of molelcules
Total (without water)7,1861
Polymers7,1861
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.800, 41.800, 92.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ALPHA-SPECTRIN


Mass: 7186.223 Da / Num. of mol.: 1 / Fragment: SRC HOMOLOGY 3 DOMAIN
Mutation: CIRCULAR PERMUTANT, CUT AT S19-P20, INS(MG-P20), INS(SG-T4)
Source method: isolated from a genetically manipulated source
Details: THIS IS A CIRCULAR PERMUTANT OF THE WT ALPHA-SPECTRIN SH3 SEQUENCE (PDB ENTRY WT-3D STRUCTURE: 1SGB). THE RESIDUE NUMBERS ARE AS IN THE WT SPECTRIN-SH3 DOMAIN (1SGB). THR 4 (N-TERMINUS) AND ...Details: THIS IS A CIRCULAR PERMUTANT OF THE WT ALPHA-SPECTRIN SH3 SEQUENCE (PDB ENTRY WT-3D STRUCTURE: 1SGB). THE RESIDUE NUMBERS ARE AS IN THE WT SPECTRIN-SH3 DOMAIN (1SGB). THR 4 (N-TERMINUS) AND ASP 62 (C-TERMINUS) OF THE WT-SH3 SEQUENCE ARE LINKED BY TWO ADDITIONAL RESIDUES (SER 2, GLY 3). THE CHAIN IS CLEAVED BETWEEN SER 19 AND PRO 20. TWO RESIDUES ARE ADDED AT THE NEW N-TERMINUS (MET 100, GLY 101).
Source: (gene. exp.) Gallus gallus (chicken) / Organ: BRAIN / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P07751
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A CIRCULAR PERMUTANT OF THE WT ALPHA-SPECTRIN SH3 SEQUENCE (PDB ENTRY WT-3D STRUCTURE: 1SGB) ...THIS IS A CIRCULAR PERMUTANT OF THE WT ALPHA-SPECTRIN SH3 SEQUENCE (PDB ENTRY WT-3D STRUCTURE: 1SGB). THE RESIDUE NUMBERS ARE AS IN THE WT SPECTRIN-SH3 DOMAIN (1SGB). THR 4 (N-TERMINUS) AND ASP 62 (C-TERMINUS) OF THE WT-SH3 SEQUENCE ARE LINKED BY TWO ADDITIONAL RESIDUES (SER 2, GLY 3). THE CHAIN IS CLEAVED BETWEEN SER 19 AND PRO 20. TWO RESIDUES ARE ADDED AT THE NEW N-TERMINUS (MET 100, GLY 101).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 64 %
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→100 Å / Num. obs: 5738 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.02→8 Å / σ(F): 1
Details: THE TWO C-TERMINAL RESIDUES (LYS 18, SER 19) ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP. THERE IS NO SIDE CHAIN ELECTRON DENSITY FOR GLU 17.
RfactorNum. reflection
Rfree0.29 -
Rwork0.214 -
obs0.214 5675
Displacement parametersBiso mean: 29.88 Å2
Refinement stepCycle: LAST / Resolution: 2.02→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 0 70 554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.577
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.262
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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