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- PDB-1e7o: A-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V44I, V58L MUTATIONS -

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Basic information

Entry
Database: PDB / ID: 1e7o
TitleA-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V44I, V58L MUTATIONS
ComponentsSPECTRIN ALPHA CHAIN
KeywordsSTRUCTURAL PROTEIN / SH3-DOMAIN / CYTOSKELETON / CALMODULIN-BINDING / ACTIN-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 / 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 chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsVega, M.C. / Serrano, L.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: A Thermodynamic and Kinetic Analysis of the Folding Pathway of an SH3 Domain Entropically Stabilised by a Redesigned Hydrophobic Core
Authors: Cobos, E.S. / Filimonov, V.V. / Vega, M.C. / Mateo, P.L. / Serrano, L. / Martinez, J.C.
#1: Journal: Nature / Year: 1992
Title: Crystal Structure of a Src-Homology 3 (SH3) Domain
Authors: Musacchio, A. / Noble, M. / Pauptit, R. / Wierenga, R. / Saraste, M.
History
DepositionAug 31, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2003Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPECTRIN ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3592
Polymers7,2671
Non-polymers921
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.000, 41.760, 52.520
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 / FODRIN ALPHA CHAIN / SPECTRIN / NON-ERYTHROID ALPHA CHAIN


Mass: 7267.313 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) / Plasmid: PBR322 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION ALA 974 VAL, VAL 986 LEU, MET 988 VAL, VAL 1007 ILE AND VAL 1021 LEU ...CHAIN A ENGINEERED MUTATION ALA 974 VAL, VAL 986 LEU, MET 988 VAL, VAL 1007 ILE AND VAL 1021 LEU BIND ACTIN BUT DIFFER IN THEIR CALMODULIN-BINDING ACTIVITY

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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: 2.25 Å3/Da / Density % sol: 45.5 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED FROM 1.1 M AMMONIUM SULPHATE, 90MM SODIUM CITRATE/CITRIC ACID, PH=6.0, 90 MM BIS-TRIS PROPANE, 0.9 MM EDTA, 0.9 MM DTT, 0.9 MM SODIUM AZIDE, pH 6.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ammonium sulfate1reservoir
2PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2000 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→12 Å / Num. obs: 1003 / % possible obs: 82.9 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.134
Reflection shellResolution: 3.2→3.5 Å / Rmerge(I) obs: 0.138 / % possible all: 77.1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 1172

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SHG

1shg


Resolution: 3.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE FIRST RESIDUE IN N-TERMINAL WAS NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 -5 %RANDOM
Rwork0.234 ---
obs0.234 1003 79.6 %-
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms487 0 6 20 513
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.559
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.788
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.288
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.2→3.34 Å
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 1172 / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.2334
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.788
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.288

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