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- PDB-3edt: Crystal structure of the mutated S328N hKLC2 TPR domain -

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Basic information

Entry
Database: PDB / ID: 3edt
TitleCrystal structure of the mutated S328N hKLC2 TPR domain
ComponentsKinesin light chain 2
KeywordsMOTOR PROTEIN / TRANSPORT PROTEIN / superhelical / Structural Genomics / 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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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: Crystal structure of mutated S328N TPR domain of human kinesin light chain 2
Authors: Zhu, H. / Shen, Y. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Kinesin light chain 2
D: Kinesin light chain 2
F: Kinesin light chain 2
H: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)128,0815
Polymers128,0814
Non-polymers01
Water30617
1
B: Kinesin light chain 2
D: Kinesin light chain 2

F: Kinesin light chain 2
H: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)128,0815
Polymers128,0814
Non-polymers01
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area7290 Å2
ΔGint-36 kcal/mol
Surface area48490 Å2
MethodPISA
2
B: Kinesin light chain 2
D: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)64,0413
Polymers64,0412
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-11 kcal/mol
Surface area24790 Å2
MethodPISA
3
F: Kinesin light chain 2
H: Kinesin light chain 2


Theoretical massNumber of molelcules
Total (without water)64,0412
Polymers64,0412
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-12 kcal/mol
Surface area24670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.202, 101.202, 115.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Kinesin light chain 2 / KLC 2


Mass: 32020.271 Da / Num. of mol.: 4 / Fragment: UNP residues 217-480 / Mutation: S328N
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): BL21 Coden(+) / References: UniProt: Q9H0B6
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7
Details: 2.0 M ammonium Sulfate, 20% Ethylene Glycol, 0.1 M Bis-Tris propane, pH 7.0, EVAPORATION, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
41
1,2,3,41
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0809 Å
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
3x-ray1
4x-ray1
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 32746
Reflection shellHighest resolution: 2.7 Å

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.912 / SU B: 37.171 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 3.162 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26691 1733 5 %RANDOM
Rwork0.22973 ---
obs0.23157 32746 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 1.998 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20.61 Å20 Å2
2--1.22 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8077 0 1 17 8095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228205
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.97711050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.49251013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50224.271398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.543151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0951568
X-RAY DIFFRACTIONr_chiral_restr0.0630.21218
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.23658
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.25507
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3660.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.55251
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it028113
X-RAY DIFFRACTIONr_scbond_it033286
X-RAY DIFFRACTIONr_scangle_it04.52937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 89 -
Rwork0.292 1677 -
obs--67.4 %
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)
18.4053-0.6867-0.13359.59621.25634.3080.27040.63020.1766-0.4614-0.2680.04840.05350.047-0.00240.09140.0861-0.0445-0.00710.00190.576215.89422.208-22.042
22.1693-1.66780.90057.2132-3.38882.06830.0019-0.03840.294-0.019-0.1615-0.3981-0.19530.07920.1595-0.01680.05930.00150.0378-0.07740.741931.15-0.746-14.014
37.2089-7.32712.85412.4809-6.899512.9106-0.043-2.4464-0.35033.3992-0.59811.9326-0.0889-0.71570.64110.47940.17670.2930.8825-0.04061.139227.479-24.829.5
420.46191.2538-0.680216.15862.85763.1837-0.1881-0.3144-0.64180.4057-0.07230.64750.3573-0.0380.2604-0.16910.05660.04870.16830.08990.736621.226-23.8170.504
54.58482.8552-0.27342.4959-2.35456.66370.6584-0.36580.727-0.4049-0.2687-0.2007-0.13050.1138-0.38970.0729-0.0458-0.013-0.0392-0.05710.831312.39730.733-13.833
61.57691.9568-0.92228.093-2.20930.7395-0.11990.0571-0.28830.10130.06540.47170.0479-0.04430.05440.0555-0.0103-0.01890.03270.01510.8013-0.8835.904-3.632
710.94940.06241.32319.655-3.399115.0712-0.11440.8632-1.42-1.2682-0.52940.49741.70610.5760.64390.29420.09510.28750.3538-0.26471.41951.425-29.73-4.333
819.61530.654-6.78068.5442-5.335413.8652-0.2708-0.0948-0.82030.3113-0.03920.45020.51340.34310.31-0.1443-0.01460.01460.0014-0.01810.9017.785-23.2531.962
99.39022.22061.57566.3741-0.73066.89710.2964-0.9304-0.41761.13-0.1440.1535-0.22120.3141-0.15240.1497-0.07660.0285-0.01360.06590.6655-33.506-54.10618.417
101.84352.1637-0.45275.6021-2.2871.2953-0.00580.0115-0.29730.1068-0.1993-0.40990.16910.0780.20510.0177-0.01940.02980.0435-0.06370.7608-20.666-29.57810.59
118.2856-0.6613-1.094615.9626-0.54847.3167-0.41481.67680.3711-2.42770.23791.1690.21360.32950.17680.5545-0.0667-0.14580.69310.12890.9496-22.86-5.349-13.92
1214.5502-1.35590.677214.42012.74696.6569-0.20020.23750.7049-0.4091-0.220.6925-0.1192-0.08030.4202-0.0982-0.0396-0.05050.12920.04430.7639-29.412-5.405-4.774
1312.7192-0.4805-0.64372.5298-1.92483.85070.5528-0.2665-0.4236-0.1912-0.299-0.19570.37450.1897-0.25390.08660.0205-0.0144-0.008-0.06370.7221-39.285-59.7379.756
141.7778-2.48710.7958.9249-2.18940.5686-0.164-0.05520.27410.03730.11510.3987-0.0423-0.02930.04890.06530.01340.00860.04380.02320.7801-51.576-34.331-0.711
1516.2015-6.51950.799514.2464-2.646115.62630.006-1.40881.24510.6077-1.12950.2481-1.24162.07741.12350.3506-0.1717-0.24550.0966-0.32221.4125-48.410.985-0.841
1617.63662.69227.77628.0714-7.290712.8107-0.4351-0.06631.0923-0.27620.07050.3409-0.43980.53480.3647-0.15870.0379-0.0298-0.0021-0.01450.9473-42.831-5.969-6.263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA210 - 25513 - 58
2X-RAY DIFFRACTION2BA256 - 39759 - 200
3X-RAY DIFFRACTION3BA398 - 447201 - 250
4X-RAY DIFFRACTION4BA448 - 479251 - 282
5X-RAY DIFFRACTION5DB211 - 23614 - 39
6X-RAY DIFFRACTION6DB237 - 39740 - 200
7X-RAY DIFFRACTION7DB398 - 447201 - 250
8X-RAY DIFFRACTION8DB448 - 479251 - 282
9X-RAY DIFFRACTION9FC210 - 24713 - 50
10X-RAY DIFFRACTION10FC248 - 39451 - 197
11X-RAY DIFFRACTION11FC395 - 447198 - 250
12X-RAY DIFFRACTION12FC448 - 479251 - 282
13X-RAY DIFFRACTION13HD211 - 23914 - 42
14X-RAY DIFFRACTION14HD240 - 39943 - 202
15X-RAY DIFFRACTION15HD400 - 447203 - 250
16X-RAY DIFFRACTION16HD448 - 479251 - 282

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