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- PDB-5djn: Crystal structure of the Kinesin-3 KIF13A NC-CC1 mutant - Deletio... -

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Basic information

Entry
Database: PDB / ID: 5djn
TitleCrystal structure of the Kinesin-3 KIF13A NC-CC1 mutant - Deletion of P390
ComponentsKinesin-like protein
KeywordsTRANSPORT PROTEIN / Coil-coil
Function / homology
Function and homology information


vesicle cargo loading / melanosome organization / microtubule motor activity / endosome to lysosome transport / microtubule-based movement / regulation of cytokinesis / intracellular protein transport / midbody / microtubule binding / endosome membrane ...vesicle cargo loading / melanosome organization / microtubule motor activity / endosome to lysosome transport / microtubule-based movement / regulation of cytokinesis / intracellular protein transport / midbody / microtubule binding / endosome membrane / centrosome / ATP binding
Similarity search - Function
Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Kinesin-associated / Kinesin-associated / 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
Similarity search - Domain/homology
Kinesin family member 13A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å
AuthorsRen, J.Q. / Feng, W.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Correlation of the Neck Coil with the Coiled-coil (CC1)-Forkhead-associated (FHA) Tandem for Active Kinesin-3 KIF13A
Authors: Ren, J. / Huo, L. / Wang, W. / Zhang, Y. / Li, W. / Lou, J. / Xu, T. / Feng, W.
History
DepositionSep 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein
C: Kinesin-like protein


Theoretical massNumber of molelcules
Total (without water)21,4062
Polymers21,4062
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-39 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.620, 158.620, 82.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Kinesin-like protein


Mass: 10703.062 Da / Num. of mol.: 2 / Fragment: UNP residues 355-445 / Mutation: P390 Deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif13a / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: F8VQ75
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 4.72 Å3/Da / Density % sol: 73.92 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7 / Details: 1.7M ammonium sulphate, 8% (v/v) isopropanol / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 9716 / % possible obs: 100 % / Redundancy: 16.1 % / Net I/σ(I): 18.7
Reflection shellResolution: 2.82→2.97 Å / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
xia2data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.82→45.79 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 970 10 %
Rwork0.1844 8732 -
obs0.1892 9702 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.4 Å2 / Biso mean: 85.8909 Å2 / Biso min: 40.72 Å2
Refinement stepCycle: final / Resolution: 2.82→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 0 16 1299
Biso mean---74 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091287
X-RAY DIFFRACTIONf_angle_d1.1231711
X-RAY DIFFRACTIONf_chiral_restr0.039197
X-RAY DIFFRACTIONf_plane_restr0.005219
X-RAY DIFFRACTIONf_dihedral_angle_d17.607538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8203-2.9690.3391380.267712341372100
2.969-3.15490.28531360.227812351371100
3.1549-3.39840.29721380.219812331371100
3.3984-3.74030.24071360.189312391375100
3.7403-4.28120.181400.152312491389100
4.2812-5.39250.21381390.159912501389100
5.3925-45.79570.23261430.18711292143599
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)
11.7655-1.3672-3.92311.2043.24389.0110.19390.1709-0.059-0.12540.80960.55560.78590.3584-0.87810.7676-0.0963-0.02911.251-0.6461.8083-24.247761.03147.4216
28.0235-3.6653-1.50333.26350.72190.99910.0531-0.36170.7144-0.0166-0.0682-0.2144-0.0054-0.02090.00750.50930.0425-0.0240.6203-0.11040.38929.425347.1924-5.4044
35.3598-0.9098-2.07721.13751.26941.8909-0.12450.7367-0.8563-0.028-0.26970.51890.0493-0.33190.43010.46560.00280.01260.55-0.11080.438522.015244.7151-8.1965
40.00250.00080.02-0.00010.00420.12010.1873-0.7227-0.61820.70720.25250.2533-0.23710.4589-0.37911.39450.5617-0.32671.7045-0.19471.121175.009424.1963-4.9164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 363 through 367 )A363 - 367
2X-RAY DIFFRACTION2chain 'A' and (resid 368 through 439 )A368 - 439
3X-RAY DIFFRACTION3chain 'C' and (resid 361 through 436 )C361 - 436
4X-RAY DIFFRACTION4chain 'C' and (resid 437 through 441 )C437 - 441

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