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- PDB-4bn2: The crystal structure of kinesin-like protein KIF15 -

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Basic information

Entry
Database: PDB / ID: 4bn2
TitleThe crystal structure of kinesin-like protein KIF15
ComponentsKINESIN-LIKE PROTEIN KIF15
KeywordsMOTOR PROTEIN / KINESIN / MOTOR DOMAIN
Function / homology
Function and homology information


plus-end kinesin complex / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / microtubule-based movement / cytoskeletal motor activity / MHC class II antigen presentation / spindle / mitotic cell cycle ...plus-end kinesin complex / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / microtubule-based movement / cytoskeletal motor activity / MHC class II antigen presentation / spindle / mitotic cell cycle / microtubule binding / microtubule / centrosome / ATP hydrolysis activity / ATP binding / membrane / cytosol
Similarity search - Function
Hyaluronan-mediated motility receptor, C-terminal / Kinesin-like protein KIF15/KIN-12E / Hyaluronan mediated motility receptor C-terminal / Kinesin motor domain / Kinesin / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Hyaluronan-mediated motility receptor, C-terminal / Kinesin-like protein KIF15/KIN-12E / Hyaluronan mediated motility receptor C-terminal / Kinesin motor domain / Kinesin / 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
ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein KIF15
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsKlejnot, M. / Falnikar, A. / Ulaganathan, V. / Cross, R. / Baas, P. / Kozielski, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Crystal Structure and Biochemical Characterization of Kif15: A Bifunctional Molecular Motor Involved in Bipolar Spindle Formation and Neuronal Development
Authors: Klejnot, M. / Falnikar, A. / Ulaganathan, V. / Cross, R.A. / Baas, P.W. / Kozielski, F.
History
DepositionMay 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references / Structure summary
Revision 2.0Oct 16, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns / reflns_shell
Item: _atom_site.occupancy / _exptl_crystal_grow.temp ..._atom_site.occupancy / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KIF15
B: KINESIN-LIKE PROTEIN KIF15
C: KINESIN-LIKE PROTEIN KIF15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4789
Polymers118,1233
Non-polymers1,3556
Water3,657203
1
A: KINESIN-LIKE PROTEIN KIF15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8263
Polymers39,3741
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KINESIN-LIKE PROTEIN KIF15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8263
Polymers39,3741
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: KINESIN-LIKE PROTEIN KIF15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8263
Polymers39,3741
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.080, 90.080, 249.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-2013-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 10:26 OR RESSEQ 33:109 OR RESSEQ...
211CHAIN B AND (RESSEQ 10:26 OR RESSEQ 33:109 OR RESSEQ...
311CHAIN C AND (RESSEQ 10:26 OR RESSEQ 33:109 OR RESSEQ...

NCS oper:
IDCodeMatrixVector
1given(0.999959, 0.007568, 0.004923), (0.00751, -0.999903, 0.011759), (0.005012, -0.011721, -0.999919)3.275, -0.758, -83.307
2given(-0.496436, -0.867199, 0.038936), (0.867886, -0.49676, 0.001552), (0.017995, 0.034563, 0.99924)-1.859, -1.114, 1.606

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Components

#1: Protein KINESIN-LIKE PROTEIN KIF15 / KINESIN / KINESIN-LIKE PROTEIN 2 / HKLP2 / KINESIN-LIKE PROTEIN 7 / SEROLOGICALLY DEFINED BREAST ...KINESIN / KINESIN-LIKE PROTEIN 2 / HKLP2 / KINESIN-LIKE PROTEIN 7 / SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-62


Mass: 39374.340 Da / Num. of mol.: 3 / Fragment: MOTOR DOMAIN, RESIDUES 19-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM20MOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: Q9NS87
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1 TO 4 CHANGED DUE TO CLONING

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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: 2.74 Å3/Da / Density % sol: 57.22 % / Description: NONE
Crystal growTemperature: 292 K / pH: 6
Details: 25% POLYETHYLENE GLYCOL-3350 0.20 M MAGNESIUM CHLORIDE 0.1 M TRIS-HC; PH 8.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 29592 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 37.87 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.6
Reflection shellHighest resolution: 2.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.1 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5C

1t5c


Resolution: 2.695→29.486 Å / SU ML: 0.88 / σ(F): 1.34 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 765 2.6 %
Rwork0.2018 --
obs0.2033 29564 88.93 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.074 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5472 Å20 Å20 Å2
2--1.5472 Å20 Å2
3----3.0944 Å2
Refinement stepCycle: LAST / Resolution: 2.695→29.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7256 0 84 203 7543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137491
X-RAY DIFFRACTIONf_angle_d1.75610135
X-RAY DIFFRACTIONf_dihedral_angle_d17.7732691
X-RAY DIFFRACTIONf_chiral_restr0.1421192
X-RAY DIFFRACTIONf_plane_restr0.0091283
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2357X-RAY DIFFRACTIONPOSITIONAL
12B2357X-RAY DIFFRACTIONPOSITIONAL0.087
13C2283X-RAY DIFFRACTIONPOSITIONAL0.076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.695-2.90290.39451400.29415505X-RAY DIFFRACTION86
2.9029-3.19470.29591590.22585578X-RAY DIFFRACTION88
3.1947-3.65630.24711420.18535757X-RAY DIFFRACTION90
3.6563-4.60370.21731570.17656004X-RAY DIFFRACTION92
4.6037-29.48730.25031670.19685955X-RAY DIFFRACTION88

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