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- PDB-3brl: Crystal Structure of LC8 S88E / Swa -

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Basic information

Entry
Database: PDB / ID: 3brl
TitleCrystal Structure of LC8 S88E / Swa
Components
  • Dynein light chain 1, cytoplasmic
  • Protein swallow 10-resiude peptide
KeywordsMOTOR PROTEIN / protein-peptide complex / Cytoplasm / Dynein / Microtubule / Cell cycle / Cell division / Developmental protein / Mitosis / Nucleus
Function / homology
Function and homology information


pole plasm mRNA localization / bicoid mRNA localization / spermatid nucleus elongation / chaeta morphogenesis / regulation of pole plasm oskar mRNA localization / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...pole plasm mRNA localization / bicoid mRNA localization / spermatid nucleus elongation / chaeta morphogenesis / regulation of pole plasm oskar mRNA localization / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / microtubule anchoring at centrosome / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / anterior/posterior axis specification, embryo / Neutrophil degranulation / dynein complex / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / dynein complex binding / oogenesis / establishment of mitotic spindle orientation / actin filament bundle assembly / centriole / actin filament organization / disordered domain specific binding / spermatogenesis / microtubule / cell cycle / cell division / mRNA binding / protein homodimerization activity / protein-containing complex / nucleus / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain type 1 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein swallow / Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBenison, G.C. / Karplus, P.A. / Barbar, E.J. / Chiodo, M.
CitationJournal: To be Published
Title: The Interplay of Ligand Binding and Phosphorylation in the Regulation of Dynein Light Chain LC8
Authors: Benison, G.C. / Chiodo, M. / Karplus, P.A. / Barbar, E.J.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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 1.3Feb 21, 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: Dynein light chain 1, cytoplasmic
C: Protein swallow 10-resiude peptide


Theoretical massNumber of molelcules
Total (without water)11,4252
Polymers11,4252
Non-polymers00
Water1,42379
1
A: Dynein light chain 1, cytoplasmic
C: Protein swallow 10-resiude peptide

A: Dynein light chain 1, cytoplasmic
C: Protein swallow 10-resiude peptide


Theoretical massNumber of molelcules
Total (without water)22,8504
Polymers22,8504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4820 Å2
ΔGint-20 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.194, 44.194, 203.218
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations: -y, -x, -z - 1/6

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Components

#1: Protein Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / Cut up protein


Mass: 10430.885 Da / Num. of mol.: 1 / Mutation: S88E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: Q24117
#2: Protein/peptide Protein swallow 10-resiude peptide


Mass: 994.034 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence can be naturally found in Drosophila melanogaster (Fruit fly)
References: UniProt: P40688
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Calcium acetate 0.2M, sodium cacodylate 0.1M, 15% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 10183 / % possible obs: 100 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.9→30.57 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.728 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 485 4.8 %RANDOM
Rwork0.191 ---
obs0.194 10090 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 0 79 880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022818
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9321103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33924.87841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45615149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.747153
X-RAY DIFFRACTIONr_chiral_restr0.0750.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02618
X-RAY DIFFRACTIONr_nbd_refined0.2120.3399
X-RAY DIFFRACTIONr_nbtor_refined0.3140.5565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.5100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.517
X-RAY DIFFRACTIONr_mcbond_it4.412502
X-RAY DIFFRACTIONr_mcangle_it5.2583791
X-RAY DIFFRACTIONr_scbond_it5.7022356
X-RAY DIFFRACTIONr_scangle_it7.613310
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 34 -
Rwork0.22 685 -
all-719 -
obs--100 %

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