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- PDB-3ceq: The TPR domain of Human Kinesin Light Chain 2 (hKLC2) -

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Basic information

Entry
Database: PDB / ID: 3ceq
TitleThe TPR domain of Human Kinesin Light Chain 2 (hKLC2)
ComponentsKinesin light chain 2
KeywordsMOTOR PROTEIN / TRANSPORT PROTEIN / HELIX TURN HELIX / Structural Genomics Consortium / SGC / Microtubule / Phosphoprotein / TPR repeat
Function / homology
Function and homology information


kinesin I complex / lysosome localization / Kinesins / RHO GTPases activate KTN1 / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / kinesin binding / MHC class II antigen presentation / microtubule ...kinesin I complex / lysosome localization / Kinesins / RHO GTPases activate KTN1 / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / kinesin binding / MHC class II antigen presentation / microtubule / cadherin binding / lysosomal membrane / protein-containing complex / mitochondrion / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...Kinesin light chain / Kinesin light chain repeat / Kinesin light chain 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsZhu, H. / Shen, Y. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The TPR domain of Human Kinesin Light Chain 2 (hKLC2)
Authors: Zhu, H. / Shen, Y. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,9872
Polymers63,9872
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-12.7 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.422, 99.940, 103.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kinesin light chain 2 / KLC 2


Mass: 31993.252 Da / Num. of mol.: 2 / Fragment: TPR Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLC2 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Coden(+) / References: UniProt: Q9H0B6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 1.46 M Ammonium Sulfate, 0.2 M Sodium Acetate, 0.1 M Bis-Tris pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.979 Å
DetectorDate: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21563 / % possible obs: 94.3 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.144 / Χ2: 8.42 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.694.20.583153811.551168.8
2.69-2.85.80.41218481.47182.2
2.8-2.937.90.32520691.918192.1
2.93-3.0811.30.31922131.558198.8
3.08-3.2815.60.29422731.8631100
3.28-3.5317.90.27722724.7291100
3.53-3.8814.60.312228123.5191100
3.88-4.4517.20.11922957.3281100
4.45-5.617.20.10323188.4331100
5.6-50160.07245614.512199.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 38.674 / SU ML: 0.336 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.976 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Atomic B factors are residuals from TLS refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 979 5.1 %RANDOM
Rwork0.234 ---
obs0.236 19197 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 0 2 4087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224156
X-RAY DIFFRACTIONr_angle_refined_deg0.8451.9745604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1965515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50724.242198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53215761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6091532
X-RAY DIFFRACTIONr_chiral_restr0.0570.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023130
X-RAY DIFFRACTIONr_nbd_refined0.1780.21844
X-RAY DIFFRACTIONr_nbtor_refined0.290.22811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.26
X-RAY DIFFRACTIONr_mcbond_it0.181.52659
X-RAY DIFFRACTIONr_mcangle_it0.32524108
X-RAY DIFFRACTIONr_scbond_it0.45831681
X-RAY DIFFRACTIONr_scangle_it0.8044.51496
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 46 -
Rwork0.33 1084 -
all-1130 -
obs--79.8 %
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)
15.6023-2.69542.96023.0413-2.13692.4435-0.02310.50220.5720.0776-0.4251-0.7907-0.17250.38440.44820.0422-0.0645-0.03890.05420.01640.350216.4343-9.31915.3435
210.2886-3.4156-0.66832.1621.31635.0010.23630.39740.26580.0235-0.1673-0.42740.1644-0.1186-0.0690.037-0.0715-0.0191-0.15330.0716-0.2227-9.87940.31197.8472
310.23-6.21963.899823.86881.888812.6742-0.09810.3254-1.722-0.33160.79472.40731.4602-1.2044-0.69670.1339-0.2893-0.01650.52870.10820.1438-33.3346-2.759810.9227
48.9643-2.3321-0.30119.70522.434512.7072-0.25410.11110.00030.39030.54650.18340.7353-0.7302-0.2924-0.1482-0.02510.01840.03680.0244-0.2448-25.12063.464519.6024
58.641-1.5866-2.72293.8581.38747.2444-0.9401-0.5827-0.52680.35770.2466-0.07140.35280.46570.69350.11810.08750.0805-0.0587-0.0360.266716.9408-23.381532.9458
63.9174-2.725-4.04332.34494.21748.565-0.4106-0.3214-0.67940.06110.0989-0.01640.54580.31960.31180.11810.02950.06450.1757-0.04480.22992.9592-17.643.9724
78.7097-5.38921.21644.64751.223.9319-0.3363-0.3251-0.2621-0.31140.2934-0.2711-0.24920.25140.04290.0111-0.08150.1162-0.04660.052-0.2072-12.191-5.179145.0687
80.11880.6548-1.043213.827-4.70129.2713-0.1616-0.16481.1732-0.08010.328-0.322-1.2681-0.8249-0.16640.25760.0780.05940.2098-0.04710.2766-27.371914.191937.0389
96.7414-0.01070.8095.5134-2.994116.80740.1365-0.13540.0467-0.12080.18390.289-0.0176-0.5231-0.3204-0.06130.05240.0034-0.0558-0.0272-0.2304-26.09863.073733.343
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA211 - 32514 - 128
2X-RAY DIFFRACTION2AA326 - 396129 - 199
3X-RAY DIFFRACTION3AA397 - 442200 - 245
4X-RAY DIFFRACTION4AA445 - 479248 - 282
5X-RAY DIFFRACTION5BB211 - 27914 - 82
6X-RAY DIFFRACTION6BB280 - 32183 - 124
7X-RAY DIFFRACTION7BB322 - 400125 - 203
8X-RAY DIFFRACTION8BB401 - 447204 - 250
9X-RAY DIFFRACTION9BB448 - 479251 - 282

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