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- PDB-6trl: Human Eg5 motor domain mutant Y82F -

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Basic information

Entry
Database: PDB / ID: 6trl
TitleHuman Eg5 motor domain mutant Y82F
ComponentsKinesin-like protein KIF11
KeywordsMOTOR PROTEIN / Eg5 motor domain mutant Y82F / KIF11 motor domain mutant Y82F / human syndrome associated Eg5 mutant
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / mitotic centrosome separation / Kinesins / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / mitotic centrosome separation / Kinesins / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / spindle / spindle pole / mitotic spindle / mitotic cell cycle / microtubule binding / microtubule / ciliary basal body / cell division / intracellular membrane-bounded organelle / protein kinase binding / protein-containing complex / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / 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 / NITRATE ION / DI(HYDROXYETHYL)ETHER / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGarcia-Saez, I. / Skoufias, D.A.
CitationJournal: To Be Published
Title: Human Eg5 motor domain mutant Y82F
Authors: Garcia-Saez, I. / Skoufias, D.A.
History
DepositionDec 19, 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)82,8888
Polymers81,8172
Non-polymers1,0716
Water4,179232
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4664
Polymers40,9081
Non-polymers5583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4224
Polymers40,9081
Non-polymers5143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.075, 77.430, 91.076
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 40908.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: P52732

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Non-polymers , 5 types, 238 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG3350, NaNO3, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.2→46.48 Å / Num. obs: 56409 / % possible obs: 88 % / Redundancy: 2.2 % / Biso Wilson estimate: 39.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.028 / Rrim(I) all: 0.044 / Χ2: 0.92 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / Num. unique obs: 1934 / CC1/2: 0.787 / Rpim(I) all: 0.371 / Rrim(I) all: 0.583 / Χ2: 1.02 / % possible all: 59.8

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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: 2.2→39.85 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.17
RfactorNum. reflection% reflection
Rfree0.2154 2745 4.98 %
Rwork0.1945 --
obs0.1955 55156 74.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.9 Å2 / Biso mean: 56.7638 Å2 / Biso min: 20.07 Å2
Refinement stepCycle: final / Resolution: 2.2→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 67 232 5493
Biso mean--41.25 49.35 -
Num. residues----662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.34741080.29882295240374
2.26-2.280.3226870.31661421150873
2.28-2.320.31161330.27782829296281
2.32-2.370.30421320.26992752288479
2.37-2.420.31391430.26812733287677
2.42-2.480.31021360.25472585272174
2.48-2.540.27641630.26112825298880
2.54-2.610.29711650.2442649281478
2.61-2.690.33441080.24211781188951
2.69-2.770.24651520.24982955310785
2.77-2.870.31631480.24012973312185
2.87-2.990.2491500.23062999314986
2.99-3.120.27381590.21142959311885
3.12-3.290.22781430.2042899304283
3.29-3.490.2371990.19972208230763
3.49-3.760.2444980.18022400249868
3.76-4.140.17921110.16572401251268
4.14-4.740.181720.14632614278676
4.74-5.960.18681700.16452964313485
5.97-39.850.1251680.15993169333791

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