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- PDB-6tle: Human Eg5 motor domain mutant E344K -

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Basic information

Entry
Database: PDB / ID: 6tle
TitleHuman Eg5 motor domain mutant E344K
ComponentsKinesin-like protein KIF11
KeywordsMOTOR PROTEIN / Eg5 motor domain mutant E344K / KIF11 motor domain mutant E344K / human syndrome associated Eg5 mutant
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / Kinesins / mitotic centrosome separation / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / mitotic centrosome separation / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle pole / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NITRATE ION / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGarcia-Saez, I. / Skoufias, D.A.
CitationJournal: To Be Published
Title: Human Eg5 motor domain mutant E344K
Authors: Garcia-Saez, I. / Skoufias, D.A.
History
DepositionDec 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF11
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8147
Polymers81,8492
Non-polymers9655
Water11,674648
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3763
Polymers40,9241
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4384
Polymers40,9241
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.930, 47.150, 85.500
Angle α, β, γ (deg.)93.910, 101.170, 109.230
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Kinesin-like protein KIF11 / Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / ...Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / Thyroid receptor-interacting protein 5 / TRIP-5


Mass: 40924.453 Da / Num. of mol.: 2 / Mutation: E344K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52732
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.22 Å3/Da / Density % sol: 44.73 % / Description: Long rod.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: PEG3350, NaNO3 and MES pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9666 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9666 Å / Relative weight: 1
ReflectionResolution: 1.746→44.07 Å / Num. obs: 62425 / % possible obs: 91.54 % / Redundancy: 1.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.039 / Rrim(I) all: 0.055 / Net I/σ(I): 11.2
Reflection shellResolution: 1.746→1.777 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.299 / Num. unique obs: 3118 / CC1/2: 0.843 / Rpim(I) all: 0.299 / Rrim(I) all: 0.423 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1II6

1ii6


Resolution: 1.75→44.07 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.13
Details: HOH B800,B802,B803 have been placed in a very disordered area which corresponds to a short exposed helix alpha0 in subunit A
RfactorNum. reflection% reflection
Rfree0.2352 3046 4.88 %
Rwork0.2008 --
obs0.2025 62418 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.58 Å2 / Biso mean: 28.8467 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.75→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5173 0 60 648 5881
Biso mean--23.26 35.36 -
Num. residues----658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.28881130.2582699281292
1.77-1.80.34181490.2662782293193
1.8-1.830.321530.25892681283493
1.83-1.870.32331580.23862757291593
1.87-1.90.29491460.23972736288294
1.9-1.940.28141370.22932784292193
1.94-1.980.26031280.22952761288993
1.98-2.030.27251430.22882753289693
2.03-2.080.25371210.21052746286793
2.08-2.140.25511580.21412763292193
2.14-2.20.21821320.20972686281892
2.2-2.270.25691420.2032736287892
2.27-2.350.29471550.20642708286392
2.35-2.450.24741370.22082679281691
2.45-2.560.23721210.21142706282792
2.56-2.690.2411270.21462730285792
2.69-2.860.26461390.2152740287993
2.86-3.080.24191430.20512634277789
3.08-3.390.22161330.18842614274788
3.39-3.880.17561360.17172622275889
3.88-4.890.19861500.15752545269588
4.89-44.070.21250.18992510263585

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