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- PDB-1u4q: Crystal Structure of Repeats 15, 16 and 17 of Chicken Brain Alpha... -

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Basic information

Entry
Database: PDB / ID: 1u4q
TitleCrystal Structure of Repeats 15, 16 and 17 of Chicken Brain Alpha Spectrin
ComponentsSpectrin alpha chain, brain
KeywordsSTRUCTURAL PROTEIN / alpha spectrin / three repeats of spectrin / alpha-helical linker region / 3-helix coiled-coil
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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...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 / 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, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKusunoki, H. / Minasov, G. / MacDonald, R.I. / Mondragon, A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Independent Movement, Dimerization and Stability of Tandem Repeats of Chicken Brain alpha-Spectrin
Authors: Kusunoki, H. / Minasov, G. / Macdonald, R.I. / Mondragon, A.
History
DepositionJul 26, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spectrin alpha chain, brain
B: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)73,5042
Polymers73,5042
Non-polymers00
Water8,017445
1
A: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)36,7521
Polymers36,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spectrin alpha chain, brain


Theoretical massNumber of molelcules
Total (without water)36,7521
Polymers36,7521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.030, 74.860, 66.610
Angle α, β, γ (deg.)90.00, 97.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Spectrin alpha chain, brain / Alpha Spectrin / Spectrin / non-erythroid alpha chain / Fodrin alpha chain


Mass: 36752.137 Da / Num. of mol.: 2 / Fragment: repeats 15, 16, 17 (residues 1662 to 1982)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Tissue: Brain / Plasmid: pET3d / 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.: 445 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 24% PEG 3.3K, 0.2M Lithium Sulfate, 2% MPD, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283, 287K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.005, 0.9785, 0.9633
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Silicon MirrorsMADMx-ray1
2Silicon MirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0051
20.97851
30.96331
ReflectionResolution: 2.2→26.7 Å / Num. obs: 36806 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.059 / Net I/σ(I): 7.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5351 / Rsym value: 0.257 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALAdata scaling
SHARPphasing
SOLVEphasing
CNS1.1refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→14.94 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.313 2477 RANDOM
Rwork0.223 --
obs-24938 -
Displacement parametersBiso mean: 58.5 Å2
Baniso -1Baniso -2Baniso -3
1--29.29 Å20 Å2-9.81 Å2
2--5.55 Å20 Å2
3---23.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 0 0 445 5636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.389 220 -
Rwork0.323 --
obs--97.7 %

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