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- PDB-1pwt: THERMODYNAMIC ANALYSIS OF ALPHA-SPECTRIN SH3 AND TWO OF ITS CIRCU... -

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Basic information

Entry
Database: PDB / ID: 1pwt
TitleTHERMODYNAMIC ANALYSIS OF ALPHA-SPECTRIN SH3 AND TWO OF ITS CIRCULAR PERMUTANTS WITH DIFFERENT LOOP LENGTHS: DISCERNING THE REASONS FOR RAPID FOLDING IN PROTEINS
ComponentsALPHA SPECTRIN
KeywordsCIRCULAR PERMUTANT / SH3 DOMAIN / CYTOSKELETON
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 / 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: 1.77 Å
AuthorsMartinez, J.C. / Viguera, A.R. / Berisio, R. / Wilmanns, M. / Mateo, P.L. / Filmonov, V.V. / Serrano, L.
CitationJournal: Biochemistry / Year: 1999
Title: Thermodynamic analysis of alpha-spectrin SH3 and two of its circular permutants with different loop lengths: discerning the reasons for rapid folding in proteins.
Authors: Martinez, J.C. / Viguera, A.R. / Berisio, R. / Wilmanns, M. / Mateo, P.L. / Filimonov, V.V. / Serrano, L.
History
DepositionOct 6, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA SPECTRIN


Theoretical massNumber of molelcules
Total (without water)7,0421
Polymers7,0421
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.000, 42.400, 49.700
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 ALPHA SPECTRIN / PWT


Mass: 7042.095 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN / Mutation: MGTG INSTEAD OF MDETG AT THE N-TERMINUS / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: CYTOSKELETON / Organ: BRAIN / References: UniProt: P07751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 4 / Details: pH 4
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
21.1 Mammonium sulfate1reservoir
390 mMsodium citrate/citric acid1reservoir
490 mMBis-Tris propane1reservoir
50.9 mMEDTA1reservoir
60.9 mMdithiothreitol1reservoir
70.9 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceType: OTHER / Wavelength: 1.5418
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→15 Å / Num. obs: 7163 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.1
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.9 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 43628
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SHG

1shg


Resolution: 1.77→14.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE N-TERMINUS HAD PROBABLY AN ALTERNATIVE CONFORMATION, BUT THE DENSITY WAS NOT CLEAR ENOUGH FOR MODELLING.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 335 5 %RANDOM
Rwork0.187 ---
obs0.189 7159 99.8 %-
Displacement parametersBiso mean: 22.9 Å2
Refinement stepCycle: LAST / Resolution: 1.77→14.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms504 0 0 88 592
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2232
X-RAY DIFFRACTIONp_mcangle_it2.0942.5
X-RAY DIFFRACTIONp_scbond_it1.5692.5
X-RAY DIFFRACTIONp_scangle_it2.3752.5
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.0940.15
X-RAY DIFFRACTIONp_singtor_nbd0.1950.5
X-RAY DIFFRACTIONp_multtor_nbd0.2630.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2170.5
X-RAY DIFFRACTIONp_planar_tor3.75
X-RAY DIFFRACTIONp_staggered_tor1515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor48.620
X-RAY DIFFRACTIONp_special_tor15

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