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- PDB-1cun: CRYSTAL STRUCTURE OF REPEATS 16 AND 17 OF CHICKEN BRAIN ALPHA SPECTRIN -

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Basic information

Entry
Database: PDB / ID: 1cun
TitleCRYSTAL STRUCTURE OF REPEATS 16 AND 17 OF CHICKEN BRAIN ALPHA SPECTRIN
ComponentsPROTEIN (ALPHA SPECTRIN)
KeywordsSTRUCTURAL PROTEIN / TWO REPEATS OF SPECTRIN / ALPHA HELICAL LINKER REGION / 2 TANDEM 3-HELIX COILED- COILS
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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / 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 domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / 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 domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / SH3-like domain superfamily / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsGrum, V.L. / Li, D. / MacDonald, R.I. / Mondragon, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structures of two repeats of spectrin suggest models of flexibility.
Authors: Grum, V.L. / Li, D. / MacDonald, R.I. / Mondragon, A.
History
DepositionAug 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 7, 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: PROTEIN (ALPHA SPECTRIN)
B: PROTEIN (ALPHA SPECTRIN)
C: PROTEIN (ALPHA SPECTRIN)


Theoretical massNumber of molelcules
Total (without water)73,1503
Polymers73,1503
Non-polymers00
Water12,394688
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.341, 201.145, 94.765
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (ALPHA SPECTRIN)


Mass: 24383.373 Da / Num. of mol.: 3
Fragment: REPEATS 16 AND 17 (RESIDUES 1771 TO 1982 PLUS AN N-TERMINAL MET)
Mutation: L1771V, G1827S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CHICKEN BRAIN MRNA FOR SPECTRIN ALPHA-CHAIN / Plasmid: PET8C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 4.12 Å3/Da / Density % sol: 70.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.99M AMMONIUM SULFATE, 0.12M NA, K TARTRATE, 0.1M NA CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.99 Mammonium sulfate1reservoir
20.12 Msodium potassium tartrate1reservoir
30.1 Msodium citrate1reservoir
45 mg/mlprotein1drop
510 mMHEPES1drop

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 387128 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.17 / % possible all: 79.5
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. obs: 75300 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Num. measured all: 387128
Reflection shell
*PLUS
Redundancy: 2.1 %

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Processing

Software
NameVersionClassification
X-PLORrefinement
REFMACrefinement
MLPHAREphasing
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→24.63 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 34928405.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3782 5 %RANDOM
Rwork0.22 ---
obs-75335 92.4 %-
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20 Å2
2---4.82 Å20 Å2
3---7.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5136 0 0 688 5824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1.1
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.009
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_d17.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.26
X-RAY DIFFRACTIONx_mcangle_it1.51.97
X-RAY DIFFRACTIONx_scbond_it22.11
X-RAY DIFFRACTIONx_scangle_it23.37
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 533 4.9 %
Rwork0.258 10284 -
obs--80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: 'REFMAC, X-PLOR' / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.216 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d1.77
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it1.26
X-RAY DIFFRACTIONp_scbond_it22.11
X-RAY DIFFRACTIONp_mcangle_it1.51.97
X-RAY DIFFRACTIONp_scangle_it23.37

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