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- PDB-1s35: Crystal Structure of Repeats 8 and 9 of Human Erythroid Spectrin -

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Basic information

Entry
Database: PDB / ID: 1s35
TitleCrystal Structure of Repeats 8 and 9 of Human Erythroid Spectrin
ComponentsSpectrin beta chain, erythrocyte
KeywordsSTRUCTURAL PROTEIN / two repeats of spectrin / alpha helical linker region / 3-helix coiled-coils / beta spectrin
Function / homology
Function and homology information


spectrin / spectrin-associated cytoskeleton / modification of postsynaptic actin cytoskeleton / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding / cortical actin cytoskeleton / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection ...spectrin / spectrin-associated cytoskeleton / modification of postsynaptic actin cytoskeleton / actin filament capping / Interaction between L1 and Ankyrins / ankyrin binding / cortical actin cytoskeleton / COPI-mediated anterograde transport / NCAM signaling for neurite out-growth / cell projection / structural constituent of cytoskeleton / cytoplasmic side of plasma membrane / actin filament binding / actin cytoskeleton / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynapse / glutamatergic synapse / cell surface / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain ...Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin beta chain, erythrocytic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsKusunoki, H. / MacDonald, R.I. / Mondragon, A.
CitationJournal: Structure / Year: 2004
Title: Structural insights into the stability and flexibility of unusual erythroid spectrin repeats
Authors: Kusunoki, H. / MacDonald, R.I. / Mondragon, A.
History
DepositionJan 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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: Spectrin beta chain, erythrocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4623
Polymers24,2701
Non-polymers1922
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.151, 122.151, 49.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Spectrin beta chain, erythrocyte / Beta-I spectrin


Mass: 24269.801 Da / Num. of mol.: 1 / Fragment: repeats 8 and 9 / Mutation: L1063E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPTB, SPTB1 / Plasmid: pET23d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11277
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Sodium Citrate, 0.3 M Ammonium Sulfate, 1.2-1.3 M Lithium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9796,0.9794,0.9642
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2003
RadiationMonochromator: Silicon Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97941
30.96421
ReflectionResolution: 2.4→45.92 Å / Num. all: 15165 / Num. obs: 15165 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.081 / Net I/σ(I): 7.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2156 / Rsym value: 0.279 / % possible all: 99.8

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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: 2.4→45.92 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 746 -RANDOM
Rwork0.222 ---
all-15134 --
obs-15134 99.7 %-
Solvent computationBsol: 45.4513 Å2 / ksol: 0.370815 e/Å3
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1-10.88 Å20 Å20 Å2
2--10.88 Å20 Å2
3----21.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1679 0 10 182 1871
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d16.1
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.5531.5
X-RAY DIFFRACTIONc_mcangle_it2.4562
X-RAY DIFFRACTIONc_scbond_it3.0372
X-RAY DIFFRACTIONc_scangle_it4.5582.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.349 100 -
Rwork0.307 --
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ION.TOP

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