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- PDB-1bg2: HUMAN UBIQUITOUS KINESIN MOTOR DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1bg2
TitleHUMAN UBIQUITOUS KINESIN MOTOR DOMAIN
ComponentsKINESIN
KeywordsMOTOR PROTEIN / ATPASE / MICROTUBULE ASSOCIATED
Function / homology
Function and homology information


positive regulation of voltage-gated sodium channel activity / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde neuronal dense core vesicle transport / anterograde dendritic transport of neurotransmitter receptor complex / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule / positive regulation of potassium ion transport / positive regulation of vesicle fusion ...positive regulation of voltage-gated sodium channel activity / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde neuronal dense core vesicle transport / anterograde dendritic transport of neurotransmitter receptor complex / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule / positive regulation of potassium ion transport / positive regulation of vesicle fusion / microtubule lateral binding / stress granule disassembly / positive regulation of intracellular protein transport / ATP-dependent microtubule motor activity, plus-end-directed / synaptic vesicle transport / JUN kinase binding / ciliary rootlet / centrosome localization / kinesin complex / microtubule motor activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / centriolar satellite / microtubule-based movement / axon cytoplasm / phagocytic vesicle / axonal growth cone / regulation of membrane potential / cellular response to interferon-gamma / hippocampus development / dendrite cytoplasm / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / axon guidance / microtubule / microtubule binding / vesicle / ATPase activity / cadherin binding / perinuclear region of cytoplasm / cell / membrane / ATP binding / identical protein binding / cytosol
Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / Kinesin-like protein / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin / 3-Layer(aba) Sandwich / Alpha Beta
Kinesin-1 heavy chain
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsKull, F.J. / Sablin, E.P. / Lau, R. / Fletterick, R.J. / Vale, R.D.
CitationJournal: Nature / Year: 1996
Title: Crystal structure of the kinesin motor domain reveals a structural similarity to myosin.
Authors: Kull, F.J. / Sablin, E.P. / Lau, R. / Fletterick, R.J. / Vale, R.D.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 4, 1998-
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0346
Polymers36,4051
Non-polymers6295
Water3,045169
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)48.540, 67.940, 112.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KINESIN /


Mass: 36405.070 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Organ: UBIQUITOUS / Plasmid: PET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P33176
#2: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.54 Å3/Da / Density % sol: 51.9 %
Crystal growpH: 4.6
Details: 5 MG/ML PROTEIN, 50 MM NA ACETATE PH 4.6, 75 MM KCL, 3.5% PEG 4K, 2.5 MM ATP, 10 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 30582 / % possible obs: 82.4 % / Observed criterion σ(I): 2 / Rsym value: 0.061 / Net I/σ(I): 12.5
Reflection shellResolution: 1.77→1.84 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.303 / % possible all: 49.2

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2304 10 %RANDOM
Rwork0.2159 ---
Obs0.2159 23039 82.4 %-
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3830 0 36 169 4035
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3622 129 10 %
Rwork0.2944 1289 -

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