- PDB-3b6v: Crystal structure of the motor domain of human kinesin family mem... -
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Basic information
Entry
Database: PDB / ID: 3b6v
Title
Crystal structure of the motor domain of human kinesin family member 3C in complex with ADP
Components
Kinesin-like protein KIF3C
Keywords
MOTOR PROTEIN / Kinesin / Structural Genomics Consortium / motor domain / ADP / SGC / ATP-binding / Microtubule / Nucleotide-binding
Function / homology
Function and homology information
intraciliary transport involved in cilium assembly / ciliary tip / organelle transport along microtubule / Intraflagellar transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement ...intraciliary transport involved in cilium assembly / ciliary tip / organelle transport along microtubule / Intraflagellar transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / microtubule-based movement / cytoskeletal motor activity / MHC class II antigen presentation / cilium / antigen processing and presentation of exogenous peptide antigen via MHC class II / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / 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 / P-loop containing nucleoside triphosphate hydrolase ...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 / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.86 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.189 / SU B: 28.773 / SU ML: 0.266 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.345 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Atomic temperature factors are residuals from TLS refinement. Programs coot, molprobity, scwrl have also been used in refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.274
726
3.7 %
thin shells
Rwork
0.202
-
-
-
all
0.205
-
-
-
obs
-
19837
97.2 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 22.038 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.1 Å2
0 Å2
0.73 Å2
2-
-
-0.34 Å2
0 Å2
3-
-
-
1.77 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4506
0
64
11
4581
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
4641
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2982
X-RAY DIFFRACTION
r_angle_refined_deg
1.229
1.979
6300
X-RAY DIFFRACTION
r_angle_other_deg
0.839
3
7306
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.253
5
596
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.123
24.023
174
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.758
15
728
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.027
15
25
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
761
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
5116
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
893
X-RAY DIFFRACTION
r_nbd_refined
0.203
0.2
859
X-RAY DIFFRACTION
r_nbd_other
0.184
0.2
2995
X-RAY DIFFRACTION
r_nbtor_refined
0.174
0.2
2176
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
2585
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.144
0.2
98
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.157
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.209
0.2
30
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.185
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
1.579
2
3135
X-RAY DIFFRACTION
r_mcbond_other
0.301
2
1228
X-RAY DIFFRACTION
r_mcangle_it
2.366
3
4809
X-RAY DIFFRACTION
r_scbond_it
1.498
2
1749
X-RAY DIFFRACTION
r_scangle_it
2.213
3
1491
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 (%)
2.7-2.77
0
0.289
1352
1513
89.359
2.77-2.845
0
0.268
1349
1428
94.468
2.845-2.927
0.364
134
0.233
1203
1405
95.16
2.927-3.016
0
0.213
1326
1376
96.366
3.016-3.114
0.271
111
0.217
1175
1310
98.168
3.114-3.222
0
0.222
1262
1283
98.363
3.222-3.342
0.31
103
0.214
1135
1253
98.803
3.342-3.476
0
0.212
1157
1177
98.301
3.476-3.629
0.274
40
0.184
1109
1165
98.627
3.629-3.803
0.251
51
0.191
1036
1099
98.908
3.803-4.005
0.252
76
0.196
952
1055
97.441
4.005-4.244
0
0.173
995
999
99.6
4.244-4.53
0.225
54
0.159
869
927
99.569
4.53-4.884
0
0.159
876
881
99.432
4.884-5.336
0.192
49
0.18
748
801
99.501
5.336-5.942
0.296
29
0.213
711
750
98.667
5.942-6.817
0.363
32
0.257
634
671
99.255
6.817-8.243
0.319
17
0.214
535
560
98.571
8.243-11.241
0.305
12
0.176
426
455
96.264
11.241-30
0.235
18
0.214
261
300
93
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°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)
1
3.5391
-0.7746
-1.2077
1.2915
0.2892
1.6883
0.0219
0.3594
0.0324
-0.1698
-0.0146
0.1684
-0.0548
-0.1806
-0.0073
-0.0092
0.0289
-0.0295
-0.0502
0.0249
0.0054
-20.3314
16.1811
16.731
2
2.9814
-0.0158
-0.9847
0.9583
0.0555
1.362
0.0056
-0.1573
-0.1616
0.0959
-0.0157
-0.0321
0.2099
0.1153
0.0101
0.0001
0.0637
-0.0226
-0.0621
0.0161
-0.0657
1.5945
-7.2234
38.9023
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
8 - 381
2
X-RAY DIFFRACTION
2
B
7 - 372
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