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- PDB-1h8k: A-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V53I, V58L MUTANT -

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Basic information

Entry
Database: PDB / ID: 1h8k
TitleA-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V53I, V58L MUTANT
ComponentsSPECTRIN ALPHA CHAIN
KeywordsSH3-DOMAIN / CYTOSKELETON / CALMODULIN-BINDING / ACTIN-BINDING
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
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsVega, M.C. / Serrano, L.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Conformational Strain in the Hydrophobic Core and its Implications for Protein Folding and Design
Authors: Ventura, S. / Vega, M.C. / Lacroix, E. / Angrand, I. / Spagnolo, L. / Serrano, L.
#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
DepositionFeb 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Dec 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


Theoretical massNumber of molelcules
Total (without water)7,2541
Polymers7,2541
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)24.510, 33.236, 62.609
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


Mass: 7254.271 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 BL21(DE3) (bacteria) / References: UniProt: P07751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ALA11VAL, VAL23LEU, MET25VAL, VAL53ILE, VAL58LEU CAN BIND ACTIN BUT SEEM TO ...ENGINEERED MUTATION ALA11VAL, VAL23LEU, MET25VAL, VAL53ILE, VAL58LEU CAN BIND ACTIN BUT SEEM TO DIFFER IN THEIR CALMODULIN- BINDING ACTIVITY. IN NONERYTHROID TISSUES, MAY PLAY AN IMPORTANT ROLE IN MEMBRANE ORGANIZATION.
Sequence details1SHG SWS P07751 1 - 964 NOT IN CONSTRUCT 1SHG SWS P07751 1026 - 2477 NOT IN CONSTRUCTT

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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: 1.76 Å3/Da
Crystal growpH: 4.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.1 M AMMONIUM SULPHATE, 0.1M ACETATE/AC. ACETIC, PH=4.5, 90 MM BIS-TRIS PROPANE, 0.9 MM SODIUM AZIDE, pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SMALL MARRESEARCH IMAGING PLATE / Date: Nov 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→12 Å / Num. obs: 2863 / % possible obs: 88.8 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.7→2.82 Å / % possible all: 71.3

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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: 2.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE 5 FIRST RESIDUE IN N-TERMINAL WAS NOTSEEN IN THE DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.221 -5 %RANDOM
Rwork0.211 ---
obs0.211 1353 88.8 %-
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms475 0 0 22 497
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_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.39
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.602
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP

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