- PDB-3b6u: Crystal structure of the motor domain of human kinesin family mem... -
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Basic information
Entry
Database: PDB / ID: 3b6u
Title
Crystal structure of the motor domain of human kinesin family member 3B in complex with ADP
Components
Kinesin-like protein KIF3B
Keywords
MOTOR PROTEIN / Kinesin / Structural Genomics Consortium / Motor domain / ADP / SGC / ATP-binding / Coiled coil / Microtubule / Nucleotide-binding
Function / homology
Function and homology information
kinesin II complex / intraciliary transport particle B binding / plus-end kinesin complex / small GTPase binding => GO:0031267 / intraciliary transport involved in cilium assembly / plus-end-directed vesicle transport along microtubule / ciliary tip / Intraflagellar transport / anterograde axonal transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ...kinesin II complex / intraciliary transport particle B binding / plus-end kinesin complex / small GTPase binding => GO:0031267 / intraciliary transport involved in cilium assembly / plus-end-directed vesicle transport along microtubule / ciliary tip / Intraflagellar transport / anterograde axonal transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / determination of left/right symmetry / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement / positive regulation of cytokinesis / mitotic spindle assembly / axon cytoplasm / MHC class II antigen presentation / mitotic spindle organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cilium / spindle / antigen processing and presentation of exogenous peptide antigen via MHC class II / microtubule cytoskeleton / midbody / microtubule binding / microtubule / centrosome / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.8→19.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.189 / SU B: 2.538 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs coot molprobity arp/warp have also been used in refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.233
2083
3.2 %
thin shells
Rwork
0.191
-
-
-
all
0.192
-
-
-
obs
0.192
64496
98.83 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 19.167 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.15 Å2
0 Å2
-0.35 Å2
2-
-
0.99 Å2
0 Å2
3-
-
-
-0.87 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→19.86 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5110
0
61
361
5532
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
5257
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
3447
X-RAY DIFFRACTION
r_angle_refined_deg
1.458
1.965
7149
X-RAY DIFFRACTION
r_angle_other_deg
0.958
3
8436
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.98
5
672
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.616
24.483
232
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.154
15
872
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.464
15
32
X-RAY DIFFRACTION
r_chiral_restr
0.087
0.2
830
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
5879
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1036
X-RAY DIFFRACTION
r_nbd_refined
0.203
0.2
922
X-RAY DIFFRACTION
r_nbd_other
0.196
0.2
3529
X-RAY DIFFRACTION
r_nbtor_refined
0.169
0.2
2484
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
2716
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.124
0.2
280
X-RAY DIFFRACTION
r_metal_ion_refined
0.014
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.248
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.251
0.2
66
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.108
0.2
18
X-RAY DIFFRACTION
r_mcbond_it
2.442
2
3464
X-RAY DIFFRACTION
r_mcbond_other
0.76
2
1360
X-RAY DIFFRACTION
r_mcangle_it
3.243
3
5353
X-RAY DIFFRACTION
r_scbond_it
2.879
2
2089
X-RAY DIFFRACTION
r_scangle_it
3.972
3
1789
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection all
% reflection obs (%)
1.8-1.848
0
0.273
4538
4794
94.66
1.848-1.898
0
0.238
4540
4652
97.592
1.898-1.952
0.263
413
0.212
4033
4528
98.189
1.952-2.012
0
0.199
4338
4397
98.658
2.012-2.077
0
0.186
4199
4262
98.522
2.077-2.149
0.243
343
0.18
3720
4112
98.808
2.149-2.229
0
0.168
3959
4002
98.926
2.229-2.319
0.253
298
0.172
3497
3823
99.268
2.319-2.421
0
0.178
3693
3712
99.488
2.421-2.537
0.231
264
0.186
3245
3527
99.49
2.537-2.672
0
0.191
3377
3390
99.617
2.672-2.83
0.225
193
0.206
2949
3147
99.841
2.83-3.021
0
0.199
2992
2995
99.9
3.021-3.257
0.257
174
0.202
2631
2808
99.893
3.257-3.559
0.191
136
0.196
2452
2589
99.961
3.559-3.963
0
0.177
2346
2349
99.872
3.963-4.546
0.211
95
0.15
1994
2089
100
4.546-5.496
0.193
64
0.178
1705
1769
100
5.496-7.491
0.311
57
0.245
1361
1419
99.93
7.491-19.858
0.235
46
0.206
844
895
99.441
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