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- PDB-1g2b: ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT ... -

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Basic information

Entry
Database: PDB / ID: 1g2b
TitleALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT N47-D48
ComponentsSPECTRIN ALPHA CHAIN
KeywordsMETAL BINDING PROTEIN / CAPPING PROTEIN / CALCIUM-BINDING / DUPLICATION / SH3 DOMAIN / CYTOSKELETON
Function / homology
Function and homology information


actin filament capping / costamere / 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 / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / 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 / SYNCHROTRON / AB INITIO / Resolution: 1.12 Å
AuthorsBerisio, 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
DepositionOct 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPECTRIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4174
Polymers7,1291
Non-polymers2883
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.100, 42.970, 53.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SPECTRIN ALPHA CHAIN


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 ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.12→14 Å / Num. all: 24461 / Num. obs: 24461 / % possible obs: 93.4 % / Rmerge(I) obs: 0.071
Reflection shellResolution: 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 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.202 1292 5 %
obs0.148 --
all-24461 -
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeOccupancy sum hydrogen: 442 / Occupancy sum non hydrogen: 664
Refinement stepCycle: LAST / Resolution: 1.12→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms526 0 15 158 699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0.039
LS refinement shellResolution: 1.12→14 Å
RfactorNum. reflection
Rfree0.203 1292
Rwork0.148 -
obs-24461
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

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