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- PDB-3m0u: Crystal Structure of the R21D mutant of alpha-spectrin SH3 domain... -

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Basic information

Entry
Database: PDB / ID: 3m0u
TitleCrystal Structure of the R21D mutant of alpha-spectrin SH3 domain. Hexagonal crystal obtained in sodium formate at pH 6.5.
ComponentsSpectrin alpha chain, brain
KeywordsSIGNALING PROTEIN / SH3-like barrel / Actin capping / Actin-binding / Calmodulin-binding / Cytoskeleton / Phosphoprotein / SH3 domain
Function / homology
Function and homology information


costamere / actin filament capping / 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
FORMIC ACID / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsGavira, J.A. / Camara-Artigas, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Understanding the polymorphic behaviour of a mutant of the alpha-spectrin SH3 domain by means of two 1.1 A structures
Authors: Camara-Artigas, A. / Gavira, J.A. / Casares, S. / Garcia-Ruiz, J.M. / Conejero-Lara, F. / Allen, J.P. / Martinez, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The effect of a proline residue on the rate of growth and the space group of alpha-spectrin SH3-domain crystals.
Authors: Camara-Artigas, A. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Cuadri, C. / Casares, S.
History
DepositionMar 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)7,2332
Polymers7,1871
Non-polymers461
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.929, 42.929, 127.486
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-63-

FMT

21A-64-

HOH

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Components

#1: Protein Spectrin alpha chain, brain / Spectrin / non-erythroid alpha chain / Fodrin alpha chain


Mass: 7187.138 Da / Num. of mol.: 1 / Fragment: UNP residues 965 to 1025 / Mutation: R21D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 298 K / Method: batch, under oil / pH: 6.5
Details: 2 M sodium formate, 0.1 M MES pH 6.5, batch, under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97752 Å
DetectorType: CCD ADSC_Q210 / Detector: CCD / Date: Mar 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97752 Å / Relative weight: 1
ReflectionResolution: 1.1→37.19 Å / Num. all: 29341 / Num. obs: 27903 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.78 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 12.8
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 7.1 / Num. unique all: 2330 / Rsym value: 0.094 / % possible all: 81.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SHG

1shg


Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.148 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.929 / SU B: 0.644 / SU ML: 0.014 / SU R Cruickshank DPI: 0.027 / SU Rfree: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.168 1412 5.1 %RANDOM
Rwork0.157 ---
all0.15776 27739 --
obs0.158 26450 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.45 Å2 / Biso mean: 19.748 Å2 / Biso min: 8.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 0 3 42 518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022491
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.987665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.454559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.40326.36422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3231593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.605151
X-RAY DIFFRACTIONr_chiral_restr0.1510.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021368
X-RAY DIFFRACTIONr_mcbond_it3.9781.5297
X-RAY DIFFRACTIONr_mcangle_it6.0512479
X-RAY DIFFRACTIONr_scbond_it7.9413194
X-RAY DIFFRACTIONr_scangle_it11.8224.5186
X-RAY DIFFRACTIONr_rigid_bond_restr4.543491
X-RAY DIFFRACTIONr_sphericity_free22.595342
X-RAY DIFFRACTIONr_sphericity_bonded10.8123482
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 84 -
Rwork0.308 1578 -
all-1662 -
obs--79.41 %

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