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- PDB-5ihk: Crystal Structure of the alpha spectrin SH3 domain mutant N47A -

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Basic information

Entry
Database: PDB / ID: 5ihk
TitleCrystal Structure of the alpha spectrin SH3 domain mutant N47A
ComponentsSpectrin alpha chain, non-erythrocytic 1
KeywordsSTRUCTURAL PROTEIN / SH3-like barrel
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 / 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
ACETATE ION / PROLINE / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsCamara-Artigas, A.
CitationJournal: to be published
Title: Crystal Structure of the alpha spectrin SH3 domain mutant N47A
Authors: Camara-Artigas, A.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Spectrin alpha chain, non-erythrocytic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4564
Polymers7,1861
Non-polymers2703
Water1,00956
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-11 kcal/mol
Surface area3760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.550, 42.371, 49.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spectrin alpha chain, non-erythrocytic 1 / Alpha-II spectrin / Fodrin alpha chain


Mass: 7186.218 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Details: SH3 domain / Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07751
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.69 Å3/Da / Density % sol: 54.33 % / Mosaicity: 0.12 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium Acetate, 1 M Ammonium sulphate, 1 M Proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015
Details: Pair of KB mirrors for adjustable focusing. Unfocused beam available tool
RadiationMonochromator: Channel-cut double crystal monochromator (CINEL), cryocooled, 6mm gap
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.35→19.93 Å / Num. obs: 15744 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 18.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.032 / Net I/σ(I): 32.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.35-1.3710.60.827197.4
7.39-19.939.50.019195.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M0R

3m0r


Resolution: 1.35→19.928 Å / SU ML: 0.09 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: FREE R-VALUE / σ(F): 0.57 / Phase error: 21.14
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 1477 5.04 %5
Rwork0.1589 ---
obs0.1604 15678 97.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.01 Å2 / Biso mean: 27.5182 Å2 / Biso min: 16.35 Å2
Refinement stepCycle: final / Resolution: 1.35→19.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 29 56 525
Biso mean--45.38 35.94 -
Num. residues----56
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007464
X-RAY DIFFRACTIONf_angle_d0.984631
X-RAY DIFFRACTIONf_chiral_restr0.08872
X-RAY DIFFRACTIONf_plane_restr0.00878
X-RAY DIFFRACTIONf_dihedral_angle_d14.527163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.39360.25841540.22822514266898
1.3936-1.44340.19671470.19312530267798
1.4434-1.50110.19791510.1542551270299
1.5011-1.56940.19841270.13972555268298
1.5694-1.65210.13391280.12132555268399
1.6521-1.75560.14491230.121426212744100
1.7556-1.8910.16241260.123525582684100
1.891-2.08120.18431080.13672306241488
2.0812-2.38190.15391430.14632484262797
2.3819-2.99930.18421430.183825802723100
2.9993-19.93050.22671270.16682562268999

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