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- PDB-1uue: a-SPECTRIN SH3 DOMAIN (V44T, D48G MUTANT) -

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Basic information

Entry
Database: PDB / ID: 1uue
Titlea-SPECTRIN SH3 DOMAIN (V44T, D48G MUTANT)
ComponentsSPECTRIN ALPHA CHAIN
KeywordsSH3-DOMAIN / SH3 / SPECTRIN / CYTOSKELETON / MEMBRANE / CALMODULIN-BINDING / ACTIN-BINDING / CALCIUM-BINDING
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 / Src homology 3 domains / SH3 type barrels. / EF-Hand 1, calcium-binding site / SH3-like domain superfamily / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVega, M.C. / Fernandez, A. / Wilmanns, M. / Serrano, L.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Solvation in Protein Folding Analysis: Combination of Theoretical and Experimental Approaches
Authors: Fernandez, A. / Vega, M.C. / Wilmanns, M. / Serrano, L.
#1: Journal: Nature / Year: 1992
Title: Crystal Structure of a Src-Homology 3 (SH3) Domain
Authors: Mussacchio, A. / Noble, M. / Pauptit, R. / Wierenga, R. / Saraste, M.
History
DepositionDec 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.7Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPECTRIN ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)7,1731
Polymers7,1731
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.094, 41.877, 49.616
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 / SPECTRIN NON-ERYTHROID ALPHA CHAIN / FODRIN ALPHA CHAIN


Mass: 7173.181 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 965-1025 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P07751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION VAL 1007 THR, ASP 1011 GLY

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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: 2.59 Å3/Da / Density % sol: 51.59 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.4 Mammonium sulfate1reservoir
20.1 Mcitric acid1reservoirpH5.0
310 mMTris-HCl1droppH7.5
44 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.802
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 2184 / % possible obs: 95 % / Redundancy: 4.5 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.78 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 26.3 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 31.94 Å / Num. obs: 2232 / % possible obs: 94.5 % / Redundancy: 4.5 % / Num. measured all: 10871 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
% possible obs: 85.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.083

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK2

1bk2


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.026 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 106 4.9 %RANDOM
Rwork0.24 ---
obs0.24 2184 95 %-
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å20 Å2
2---0.7 Å20 Å2
3----1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms468 0 0 24 492
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.81.5
X-RAY DIFFRACTIONc_mcangle_it10.482
X-RAY DIFFRACTIONc_scbond_it9.382
X-RAY DIFFRACTIONc_scangle_it13.692.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.082 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 17 4.7 %
Rwork0.319 345 -
obs--98 %
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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