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- PDB-1u4c: Structure of spindle checkpoint protein Bub3 -

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Basic information

Entry
Database: PDB / ID: 1u4c
TitleStructure of spindle checkpoint protein Bub3
ComponentsCell cycle arrest protein BUB3
KeywordsCELL CYCLE / WD40 protein / WD-40 protein / beta propeller
Function / homology
Function and homology information


bub1-bub3 complex / Inactivation of APC/C via direct inhibition of the APC/C complex / mitotic DNA integrity checkpoint signaling / mitotic checkpoint complex / positive regulation of protein autoubiquitination / mitotic spindle assembly checkpoint signaling / ubiquitin binding / kinetochore / nucleoplasm
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Cell cycle arrest protein BUB3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsLarsen, N.A. / Harrison, S.C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the spindle assembly checkpoint protein Bub3
Authors: Larsen, N.A. / Harrison, S.C.
History
DepositionJul 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell cycle arrest protein BUB3
B: Cell cycle arrest protein BUB3


Theoretical massNumber of molelcules
Total (without water)79,3912
Polymers79,3912
Non-polymers00
Water6,197344
1
A: Cell cycle arrest protein BUB3


Theoretical massNumber of molelcules
Total (without water)39,6951
Polymers39,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell cycle arrest protein BUB3


Theoretical massNumber of molelcules
Total (without water)39,6951
Polymers39,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.266, 73.266, 110.425
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Cell cycle arrest protein BUB3


Mass: 39695.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BUB3 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) / References: UniProt: P26449
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 3350, 100mM citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97945, 0.97958, 0.9200
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979581
30.921
ReflectionResolution: 2.35→40 Å / Num. all: 55100 / Num. obs: 52125 / % possible obs: 94.6 % / Observed criterion σ(F): 1.3 / Observed criterion σ(I): 1.7 / Redundancy: 2.9 % / Biso Wilson estimate: 65 Å2 / Rsym value: 0.057 / Net I/σ(I): 19
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.488 / % possible all: 93.2

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.35→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2142 -Random with constraint that twin related reflections are in same set (working or test)
Rwork0.196 ---
all0.211 55172 --
obs0.202 49192 89.2 %-
Displacement parametersBiso mean: 59 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5167 0 0 344 5511
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.807

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