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- PDB-5fwc: Human Spectrin SH3 domain D48G, E7A, K60A -

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Basic information

Entry
Database: PDB / ID: 5fwc
TitleHuman Spectrin SH3 domain D48G, E7A, K60A
ComponentsSPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1
KeywordsSTRUCTURAL PROTEIN / SPECTRIN SH3
Function / homology
Function and homology information


spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins ...spectrin / actin filament capping / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / RHOV GTPase cycle / cortical actin cytoskeleton / RHOU GTPase cycle / Caspase-mediated cleavage of cytoskeletal proteins / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection / structural constituent of cytoskeleton / specific granule lumen / microtubule cytoskeleton / extracellular vesicle / actin filament binding / tertiary granule lumen / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / calmodulin binding / cadherin binding / intracellular membrane-bounded organelle / calcium ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol
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
AMMONIUM ION / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGallego, P. / Navarro, S. / Ventura, S. / Reverter, D.
CitationJournal: To be Published
Title: Human Spectrin SH3 Domain D48G, E7A, K60A
Authors: Navarro, S. / Gallego, P. / Diaz, M. / Ventura, S. / Reverter, D.
History
DepositionFeb 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1974
Polymers7,0551
Non-polymers1423
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.685, 42.212, 48.963
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, NON-ERYTHROCYTIC 1 / ALPHA-II SPECTRIN / FODRIN ALPHA CHAIN / SPECTRIN / NON-ERYTHROID ALPHA SUBUNIT / HUMAN SPECTRIN SH3


Mass: 7055.070 Da / Num. of mol.: 1 / Fragment: SH3, RESIDUES 965-1022 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13813
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.14 % / Description: NONE

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Data collection

DiffractionMean temperature: 10 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979493
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 1.4→48.96 Å / Num. obs: 14310 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENRTY 1BK2

1bk2


Resolution: 1.4→31.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23811 715 5 %RANDOM
Rwork0.21432 ---
obs0.21543 13553 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.115 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2---1.43 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.4→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms459 0 9 55 523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.022500
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8091.976672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.363560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg49.83325.23821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.131595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.179152
X-RAY DIFFRACTIONr_chiral_restr0.1980.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021361
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8571.5299
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8522482
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7813201
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0184.5190
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.7183500
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.399→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 54 -
Rwork0.322 936 -
obs--99.1 %

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