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- PDB-5ojf: Crystal Structure of KLC2-TPR domain (fragment [A1-B6] -

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Basic information

Entry
Database: PDB / ID: 5ojf
TitleCrystal Structure of KLC2-TPR domain (fragment [A1-B6]
ComponentsKinesin light chain 2
KeywordsMOTOR PROTEIN / Kinesin1 / KLC2 / TPR domain
Function / homology
Function and homology information


lysosome localization / kinesin complex / microtubule / mitochondrion / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNguyen, T.Q. / Chenon, M. / Vilela, F. / Velours, C. / Andreani, J. / Fernandez-Varela, P. / Llinas, P. / Menetrey, J.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural plasticity of the N-terminal capping helix of the TPR domain of kinesin light chain.
Authors: Nguyen, T.Q. / Chenon, M. / Vilela, F. / Velours, C. / Aumont-Nicaise, M. / Andreani, J. / Varela, P.F. / Llinas, P. / Menetrey, J.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin light chain 2
B: Kinesin light chain 2
C: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)106,4103
Polymers106,4103
Non-polymers00
Water00
1
A: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)35,4701
Polymers35,4701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)35,4701
Polymers35,4701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)35,4701
Polymers35,4701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.620, 116.470, 108.110
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Kinesin light chain 2 / Klc2 protein


Mass: 35470.137 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klc2, mCG_8395 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YS4

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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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 12 % PEG 3350, 0.5 M Phos. pH 7.5 Glycerol 25 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980097 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980097 Å / Relative weight: 1
ReflectionResolution: 3.4→48.14 Å / Num. obs: 16593 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 135.76 Å2 / Rrim(I) all: 0.236 / Net I/σ(I): 4.55
Reflection shellResolution: 3.4→3.59 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.08 / Rrim(I) all: 1.168 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CEQ, 3NF1

3ceq

3nf1


Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.885 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.529
RfactorNum. reflection% reflectionSelection details
Rfree0.264 819 4.99 %RANDOM
Rwork0.232 ---
obs0.234 16409 99.9 %-
Displacement parametersBiso mean: 127.81 Å2
Baniso -1Baniso -2Baniso -3
1-24.417 Å20 Å2-5.5685 Å2
2---26.7335 Å20 Å2
3---2.3165 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: 1 / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 0 0 6255
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016360HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.198583HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2313SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes177HARMONIC2
X-RAY DIFFRACTIONt_gen_planes912HARMONIC5
X-RAY DIFFRACTIONt_it6360HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion24.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion810SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7260SEMIHARMONIC4
LS refinement shellResolution: 3.4→3.63 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.278 148 4.96 %
Rwork0.223 2836 -
all0.226 2984 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.61840.1536-4.35821.1395-0.53555.84530.017-0.76430.00160.1069-0.0792-0.40750.01880.9670.0622-0.0790.12720.1256-0.28760.2065-0.0318.10619.302914.6915
25.66780.667-3.79252.4313-0.9815.12570.1325-0.5920.26890.57350.16860.2427-0.70780.2915-0.30120.40220.03050.2957-0.5848-0.0626-0.0434-8.420533.799420.2958
35.7524-0.0724-3.57951.49440.61594.8965-0.2061-0.1682-0.8781-0.1258-0.2687-0.12690.6571-0.47070.47480.21880.15180.2268-0.30080.2765-0.002-17.6793-7.074634.5491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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