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- PDB-3nf1: Crystal structure of the TPR domain of kinesin light chain 1 -

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Basic information

Entry
Database: PDB / ID: 3nf1
TitleCrystal structure of the TPR domain of kinesin light chain 1
ComponentsKinesin light chain 1
KeywordsMOTOR PROTEIN / TRANSPORT PROTEIN / kinesin / tpr / structural genomics consortium (sgc)
Function / homology
Function and homology information


Kinesins / RHO GTPases activate KTN1 / stress granule disassembly / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / cytoskeletal motor activity / kinesin binding / Signaling by ALK fusions and activated point mutants / MHC class II antigen presentation ...Kinesins / RHO GTPases activate KTN1 / stress granule disassembly / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / cytoskeletal motor activity / kinesin binding / Signaling by ALK fusions and activated point mutants / MHC class II antigen presentation / growth cone / cytoplasmic vesicle / microtubule / cell adhesion / membrane / cytosol / cytoplasm
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Kinesin light chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsTong, Y. / Tempel, W. / Shen, L. / Shen, Y. / Nedyalkova, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Tong, Y. / Tempel, W. / Shen, L. / Shen, Y. / Nedyalkova, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the TPR domain of kinesin light chain 1
Authors: Tong, Y. / Tempel, W. / Shen, L. / Shen, Y. / Nedyalkova, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Kinesin light chain 1


Theoretical massNumber of molelcules
Total (without water)35,4391
Polymers35,4391
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.685, 74.685, 156.168
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Kinesin light chain 1 / KLC 1


Mass: 35439.105 Da / Num. of mol.: 1 / Fragment: UNP residues 203 to 497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLC1, KLC, KNS2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q07866

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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: 3.9 Å3/Da / Density % sol: 68.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M ammonium formate, 0.1M HEPES, 0.001M TCEP., pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.92015 Å
DetectorType: MAR-300 / Detector: CCD / Date: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92015 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 12665 / % possible obs: 97.2 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.068 / Χ2: 1.993 / Net I/σ(I): 15.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.8-2.93.80.5849970.924178.7
2.9-3.025.90.52611950.961194.1
3.02-3.157.80.36412721.02199.2
3.15-3.328.90.26412821.1761100
3.32-3.539.30.18212681.5011100
3.53-3.89.40.12913031.9361100
3.8-4.189.40.09112962.3811100
4.18-4.789.80.07213032.7651100
4.78-6.0210.30.06313382.5691100
6.02-309.40.03914112.951199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3CEQ

3ceq


Resolution: 2.8→29.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFMAC, phenix, coot and the molprobity server were also used during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.273 583 4.63 %thin shells (sftools)
Rwork0.2 ---
obs0.204 12597 --
Displacement parametersBiso mean: 94.53 Å2
Baniso -1Baniso -2Baniso -3
1-12.708 Å20 Å20 Å2
2--12.708 Å20 Å2
3----25.416 Å2
Refine analyzeLuzzati coordinate error obs: 0.468 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 0 0 2149
LS refinement shellResolution: 2.8→3.07 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 134 5.04 %
Rwork0.264 2523 -
all0.265 2657 -

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