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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 / homologyKinesin motor domain profile. / COPI-dependent Golgi-to-ER retrograde traffic / Insulin processing / MHC class II antigen presentation / RHO GTPases activate KTN1 / Kinesin motor domain, conserved site / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain / Kinesin-like protein / Kinesin motor domain superfamily ...Kinesin motor domain profile. / COPI-dependent Golgi-to-ER retrograde traffic / Insulin processing / MHC class II antigen presentation / RHO GTPases activate KTN1 / Kinesin motor domain, conserved site / P-loop containing nucleoside triphosphate hydrolase / Kinesin motor domain / Kinesin-like protein / Kinesin motor domain superfamily / Kinesin motor domain / Kinesin motor domain signature. / Kinesins / positive regulation of voltage-gated sodium channel activity / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / vesicle transport along microtubule / positive regulation of potassium ion transport / microtubule lateral binding / positive regulation of vesicle fusion / stress granule disassembly / positive regulation of intracellular protein 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 / axon cytoplasm / microtubule-based movement / phagocytic vesicle / regulation of membrane potential / axonal growth cone / cellular response to interferon-gamma / hippocampus development / positive regulation of synaptic transmission, GABAergic / microtubule organizing center / positive regulation of protein localization to plasma membrane / microtubule / microtubule binding / vesicle / ATPase activity / cadherin binding / perinuclear region of cytoplasm / membrane / ATP binding / identical protein binding / cytosol / Kinesin-1 heavy chain
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 1.8 Å resolution
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
DateDeposition: Jun 4, 1998 / Release: Oct 14, 1998
RevisionDateData content typeGroupProviderType
1.0Oct 14, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KINESIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0346
Polyers36,4051
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-MP 21 21 21

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Components

#1: Protein/peptide KINESIN /


Mass: 36405.070 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cell line: BL21 / Organ: UBIQUITOUS / Plasmid name: PET / Genus (production host): Escherichia / 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


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Formula: C2H3O2 / Acetate
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Formula: H2O / Water

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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 / Density percent 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 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL7-1 / Synchrotron site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Collection date: Jun 1, 1995
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionD resolution high: 1.8 Å / Number obs: 30582 / Observed criterion sigma I: 2 / Rsym value: 0.061 / NetI over sigmaI: 12.5 / Percent possible obs: 82.4
Reflection shellHighest resolution: 1.77 Å / Lowest resolution: 1.84 Å / MeanI over sigI obs: 2.1 / Rsym value: 0.303 / Percent 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
RefineMethod to determine structure: MIR / R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / Sigma F: 2
Displacement parametersB iso mean: 31.5 Å2
Least-squares processR factor R free: 0.288 / R factor R work: 0.2159 / R factor obs: 0.2159 / Highest resolution: 1.8 Å / Lowest resolution: 6 Å / Number reflection R free: 2304 / Number reflection obs: 23039 / Percent reflection R free: 1 / Percent reflection obs: 82.4
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 3830 / Nucleic acid: 0 / Ligand: 36 / Solvent: 169 / Total: 4035
Refine LS shellHighest resolution: 1.8 Å / R factor R free: 0.3622 / R factor R work: 0.2944 / Lowest resolution: 1.88 Å / Number reflection R free: 129 / Number reflection R work: 1289 / Total number of bins used: 8 / Percent reflection R free: 1

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