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- PDB-3ngp: High resolution structure of alpha-spectrin SH3 domain mutant wit... -

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Basic information

Entry
Database: PDB / ID: 3ngp
TitleHigh resolution structure of alpha-spectrin SH3 domain mutant with a redesigned core
ComponentsSpectrin alpha chain, brain
KeywordsSTRUCTURAL PROTEIN / beta 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
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.084 Å
AuthorsCamara-Artigas, A. / Gavira, J.A. / Martin-Garcia, J.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: High-resolution structure of an alpha-spectrin SH3-domain mutant with a redesigned hydrophobic core.
Authors: Camara-Artigas, A. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Cuadri, C. / Cobos, E.S. / Martin-Garcia, J.M.
History
DepositionJun 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)7,2091
Polymers7,2091
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.787, 37.231, 62.949
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, brain / Spectrin / non-erythroid alpha chain / Fodrin alpha chain


Mass: 7209.277 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 965 to 1025) / Mutation: A11V, V23L, M25V, V44I,V58L,D48G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulphate, 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.08→20 Å / Num. all: 25460 / Num. obs: 25256 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.083 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.08-1.143.20.3323.235900.498.4
3.43-202.60.04523.48030.05691

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SHG

1shg


Resolution: 1.084→18.28 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 2392 5.14 %RANDOM
Rwork0.168 ---
obs0.1688 46537 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.495 Å2 / ksol: 0.482 e/Å3
Displacement parametersBiso mean: 12.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.5001 Å2-0 Å20 Å2
2---2.8756 Å2-0 Å2
3---1.3755 Å2
Refinement stepCycle: LAST / Resolution: 1.084→18.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms472 0 0 65 537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005489
X-RAY DIFFRACTIONf_angle_d1.005663
X-RAY DIFFRACTIONf_dihedral_angle_d10.078187
X-RAY DIFFRACTIONf_chiral_restr0.06375
X-RAY DIFFRACTIONf_plane_restr0.00582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0838-1.12250.2662060.23314309X-RAY DIFFRACTION94
1.1225-1.16750.22842730.20134396X-RAY DIFFRACTION98
1.1675-1.22060.18432580.18284390X-RAY DIFFRACTION98
1.2206-1.28490.19962520.15774485X-RAY DIFFRACTION99
1.2849-1.36540.16512300.14614452X-RAY DIFFRACTION98
1.3654-1.47080.16232590.13294468X-RAY DIFFRACTION99
1.4708-1.61870.1672490.12864454X-RAY DIFFRACTION99
1.6187-1.85280.14842400.13484499X-RAY DIFFRACTION99
1.8528-2.33350.14712240.13294477X-RAY DIFFRACTION98
2.3335-18.28230.19372010.18264215X-RAY DIFFRACTION92

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