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- PDB-2spc: CRYSTAL STRUCTURE OF THE REPETITIVE SEGMENTS OF SPECTRIN -

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Basic information

Entry
Database: PDB / ID: 2spc
TitleCRYSTAL STRUCTURE OF THE REPETITIVE SEGMENTS OF SPECTRIN
ComponentsSPECTRIN
KeywordsCYTOSKELETON
Function / homology
Function and homology information


oocyte construction / Caspase-mediated cleavage of cytoskeletal proteins / long-term strengthening of neuromuscular junction / spectrosome / maintenance of presynaptic active zone structure / fusome organization / germarium-derived female germ-line cyst formation / fusome / germarium-derived oocyte fate determination / COPI-mediated anterograde transport ...oocyte construction / Caspase-mediated cleavage of cytoskeletal proteins / long-term strengthening of neuromuscular junction / spectrosome / maintenance of presynaptic active zone structure / fusome organization / germarium-derived female germ-line cyst formation / fusome / germarium-derived oocyte fate determination / COPI-mediated anterograde transport / plasma membrane organization / neuromuscular synaptic transmission / Neutrophil degranulation / negative regulation of microtubule depolymerization / actin filament capping / axon midline choice point recognition / regulation of synapse organization / lateral plasma membrane / central nervous system development / neuromuscular junction / actin binding / cell cortex / regulation of cell shape / microtubule binding / basolateral plasma membrane / cytoskeleton / calmodulin binding / apical plasma membrane / calcium ion binding / Golgi apparatus / plasma membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin alpha chain
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsYan, Y. / Winograd, E. / Viel, A. / Cronin, T. / Harrison, S.C. / Branton, D.
CitationJournal: Science / Year: 1993
Title: Crystal structure of the repetitive segments of spectrin.
Authors: Yan, Y. / Winograd, E. / Viel, A. / Cronin, T. / Harrison, S.C. / Branton, D.
History
DepositionMar 1, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPECTRIN
B: SPECTRIN


Theoretical massNumber of molelcules
Total (without water)24,5852
Polymers24,5852
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-42 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.800, 47.220, 104.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-656-

HOH

21B-655-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.55, -0.835, 0.001), (-0.835, 0.55, -0.006), (0.005, -0.004, -1)
Vector: 36.22, 19.87, 114.97)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

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Components

#1: Protein SPECTRIN


Mass: 12292.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P13395
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG4001reservoir
21 Mammonium acetate1reservoir
350 mMMES1reservoir
420 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 20541 / % possible obs: 95 % / Num. measured all: 88201 / Rmerge(I) obs: 0.046

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→6 Å / Rfactor Rwork: 0.203 / Rfactor obs: 0.203 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 156 1882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.203 / Rfactor Rfree: 0.304 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_d2.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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