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- PDB-1u06: crystal structure of chicken alpha-spectrin SH3 domain -

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Basic information

Entry
Database: PDB / ID: 1u06
Titlecrystal structure of chicken alpha-spectrin SH3 domain
ComponentsSpectrin alpha chain, brain
KeywordsSTRUCTURAL PROTEIN / SH3 domain / beta barrel / five antiparallel beta sheets
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
AZIDE ION / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsChevelkov, V. / Faelber, K. / Diehl, A. / Heinemann, U. / Oschkinat, H. / Reif, B.
CitationJournal: J.Biomol.Nmr / Year: 2005
Title: Detection of dynamic water molecules in a microcrystalline sample of the SH3 domain of alpha-spectrin by MAS solid-state NMR.
Authors: Chevelkov, V. / Faelber, K. / Diehl, A. / Heinemann, U. / Oschkinat, H. / Reif, B.
History
DepositionJul 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Spectrin alpha chain, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3554
Polymers7,2291
Non-polymers1263
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.600, 42.250, 49.610
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: 7229.244 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P07751
#2: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.52 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.006231 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 17, 2003 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006231 Å / Relative weight: 1
ReflectionResolution: 1.49→40 Å / Num. all: 11423 / Num. obs: 11318 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.038 / Net I/σ(I): 23.5
Reflection shellResolution: 1.49→1.55 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 1063 / Rsym value: 0.255 / % possible all: 79.9

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
REFMAC5.1.24refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHG

1shg


Resolution: 1.49→32.11 Å
Isotropic thermal model: OVERALL ANISOTROPIC B VALUE + TLS GROUP RESIDUE RANGE 7 - 61
Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1885 791 RANDOM
Rwork0.1747 --
all0.1757 10632 -
obs0.1757 10632 -
Displacement parametersBiso mean: 14.615 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20 Å2
2---1.38 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.49→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 9 53 532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.012
X-RAY DIFFRACTIONr_angle_refined_deg1.531
X-RAY DIFFRACTIONr_mcbond_it1.199
X-RAY DIFFRACTIONr_scbond_it2.74
LS refinement shellResolution: 1.49→1.529 Å /
RfactorNum. reflection
Rfree0.234 52
Rwork0.235 -
obs-623

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