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- PDB-6ro9: Human spectrin SH3 domain D48G, E7V, K60V -

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Basic information

Entry
Database: PDB / ID: 6ro9
TitleHuman spectrin SH3 domain D48G, E7V, K60V
ComponentsSpectrin alpha, non-erythrocytic 1
KeywordsPROTEIN BINDING / Binding Domain
Function / homology
Function and homology information


clustering of voltage-gated sodium channels / paranode region of axon / node of Ranvier / actin filament capping / actin binding / cell cortex / cytoskeleton / calmodulin binding / calcium ion binding
Similarity search - Function
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / SH3 domain / EF-hand domain pair ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / 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, non-erythrocytic 1
Similarity search - Component
Biological speciesMola mola (ocean sunfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.814 Å
AuthorsReverter, D. / Navarro, S. / Ventura, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: To Be Published
Title: Human spectrin SH3 domain D48G, E7V, K60V
Authors: Reverter, D. / Navarro, S. / Ventura, S.
History
DepositionMay 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Spectrin alpha, non-erythrocytic 1


Theoretical massNumber of molelcules
Total (without water)6,9961
Polymers6,9961
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.906, 41.819, 48.798
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, non-erythrocytic 1


Mass: 6996.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mola mola (ocean sunfish) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q3W9R3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 316 K / Method: vapor diffusion, hanging drop / Details: 2M ammonium sulfate and 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.814→41.819 Å / Num. obs: 6486 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.051 / Net I/σ(I): 11.4
Reflection shellResolution: 1.814→1.82 Å / Rmerge(I) obs: 1.081 / Num. unique obs: 66 / CC1/2: 0.755 / Rpim(I) all: 0.477

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FW9

5fw9


Resolution: 1.814→31.754 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.53
RfactorNum. reflection% reflection
Rfree0.2557 327 5.07 %
Rwork0.203 --
obs0.2057 6449 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.814→31.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms456 0 0 32 488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018465
X-RAY DIFFRACTIONf_angle_d1.753630
X-RAY DIFFRACTIONf_dihedral_angle_d16.267174
X-RAY DIFFRACTIONf_chiral_restr0.0972
X-RAY DIFFRACTIONf_plane_restr0.0177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8138-2.28520.28251550.24042995X-RAY DIFFRACTION100
2.2852-31.75870.24691720.18983127X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -0.2336 Å / Origin y: 5.0522 Å / Origin z: 16.5741 Å
111213212223313233
T0.1466 Å2-0.0211 Å20.0076 Å2-0.0817 Å2-0.0222 Å2--0.1217 Å2
L4.7853 °2-1.8423 °2-0.2118 °2-6.0089 °2-0.224 °2--6.136 °2
S-0.1241 Å °-0.1172 Å °-0.0402 Å °0.1101 Å °0.0984 Å °0.0458 Å °0.1056 Å °-0.2359 Å °0.0198 Å °
Refinement TLS groupSelection details: all

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