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- PDB-2v14: Kinesin 16B Phox-homology domain (KIF16B) -

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Basic information

Entry
Database: PDB / ID: 2v14
TitleKinesin 16B Phox-homology domain (KIF16B)
ComponentsKINESIN-LIKE MOTOR PROTEIN C20ORF23
KeywordsTRANSPORT PROTEIN / PLUS-END KINESIN COMPLEX / PHOSPHATIDYLINOSITOL 3-PHOSPHATE BINDING / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / MOTOR PROTEIN / UBL CONJUGATION / ENDOSOME TRANSPORT / PLUS-END-DIRECTED MICROTUBULE MOTOR ACTIVITY / MICROTUBULE / COILED COIL / ATP-BINDING / POLYMORPHISM
Function / homology
Function and homology information


formation of primary germ layer / Golgi to endosome transport / receptor catabolic process / early endosome to late endosome transport / endoderm development / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding / Kinesins / plus-end-directed microtubule motor activity / phosphatidylinositol-3,5-bisphosphate binding ...formation of primary germ layer / Golgi to endosome transport / receptor catabolic process / early endosome to late endosome transport / endoderm development / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3-phosphate binding / Kinesins / plus-end-directed microtubule motor activity / phosphatidylinositol-3,5-bisphosphate binding / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of receptor recycling / fibroblast growth factor receptor signaling pathway / epidermal growth factor receptor signaling pathway / spindle / early endosome membrane / microtubule binding / microtubule / early endosome / endosome / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. ...Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinesin-like protein KIF16B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsWilson, M.I. / Williams, R.L. / Cho, W. / Hong, W. / Blatner, N.R.
CitationJournal: Embo J. / Year: 2007
Title: The Structural Basis of Novel Endosome Anchoring Activity of Kif16B Kinesin.
Authors: Blatner, N.R. / Wilson, M.I. / Lei, C. / Hong, W. / Murray, D. / Williams, R.L. / Cho, W.
History
DepositionMay 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KINESIN-LIKE MOTOR PROTEIN C20ORF23


Theoretical massNumber of molelcules
Total (without water)15,9281
Polymers15,9281
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.894, 100.894, 100.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein KINESIN-LIKE MOTOR PROTEIN C20ORF23 / KIF16B KINESIN-3 MOTOR PROTEIN / SORTING NEXIN-23


Mass: 15928.246 Da / Num. of mol.: 1 / Fragment: PHOX-HOMOLOGY DOMAIN, RESIDUES 1179-1312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: Q96L93
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPROBABLY INVOLVED IN SEVERAL STAGES OF INTRACELLULAR TRAFFICKING
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.2 % / Description: NONE
Crystal growpH: 8.8 / Details: 25% PEG 3350, 0.1 M TRIS PH 8.8, 0.2 M NH4OAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 , 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 3, 2006 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.93931
ReflectionResolution: 2.2→71.43 Å / Num. obs: 8819 / % possible obs: 100 % / Observed criterion σ(I): -4 / Redundancy: 27.54 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.84
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 5.15 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.17 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
TRUNCATEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.2→71.43 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.158 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.24 / Stereochemistry target values: RESTRAINED
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BETA1-BETA2 (1195-1200) LOOP HAD POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 420 4.82 %RANDOM
Rwork0.209 ---
obs0.212 8819 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 39.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→71.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 0 62 1180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221147
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9671541
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.922.26453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53315217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.992159
X-RAY DIFFRACTIONr_chiral_restr0.1020.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02853
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2433
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2786
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0761.5693
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.821090
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1453514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3044.5451
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 9.76→71.43 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 5
Rwork0.305 116

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