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- PDB-2quq: Crystal Structure of the Essential Inner Kinetochore Protein Cep3p -

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Basic information

Entry
Database: PDB / ID: 2quq
TitleCrystal Structure of the Essential Inner Kinetochore Protein Cep3p
ComponentsCentromere DNA-binding protein complex CBF3 subunit B
KeywordsDNA BINDING PROTEIN / STRUCTURAL PROTEIN / dimer / Centromere / Chromosomal protein / DNA-binding / Metal-binding / Nucleus / Phosphorylation / Zinc / PROTEIN BINDING / CELL CYCLE
Function / homology
Function and homology information


CBF3 complex / septin ring assembly / centromeric DNA binding / kinetochore assembly / DNA binding, bending / mitotic spindle assembly checkpoint signaling / kinetochore / DNA-binding transcription factor activity, RNA polymerase II-specific / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain
Similarity search - Domain/homology
Centromere DNA-binding protein complex CBF3 subunit B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsBellizzi III, J.J. / Harrison, S.C.
CitationJournal: Structure / Year: 2007
Title: Crystal structure of the yeast inner kinetochore subunit Cep3p.
Authors: Bellizzi, J.J. / Sorger, P.K. / Harrison, S.C.
History
DepositionAug 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Centromere DNA-binding protein complex CBF3 subunit B


Theoretical massNumber of molelcules
Total (without water)66,0951
Polymers66,0951
Non-polymers00
Water27015
1
A: Centromere DNA-binding protein complex CBF3 subunit B

A: Centromere DNA-binding protein complex CBF3 subunit B


Theoretical massNumber of molelcules
Total (without water)132,1892
Polymers132,1892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area5790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.629, 84.629, 230.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe biological unit is a dimer generated from the asymmetric unit by the crystallographic dyad.

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Components

#1: Protein Centromere DNA-binding protein complex CBF3 subunit B / Centromere protein 3


Mass: 66094.523 Da / Num. of mol.: 1 / Fragment: residues 47-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CBF3B, CEP3 / Plasmid: pET3aTr / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P40969
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 5% PEG 4000, 500 mM NaCl, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.07182
SYNCHROTRONAPS 24-ID-C21.00794, 1.00912
SYNCHROTRONAPS 24-ID-C31.07179, 1.07206
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 2, 2006
ADSC QUANTUM 3152CCDJul 22, 2006
ADSC QUANTUM 3153CCDJul 21, 2006
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2MADx-ray1
3MADx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.071821
21.007941
31.009121
41.071791
51.072061
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 9.8 / Number: 139991 / Rmerge(I) obs: 0.072 / Χ2: 1.09 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 20443 / % possible obs: 94.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.035097.610.0391.3986.8
4.796.0399.510.0621.5837.1
4.184.7999.510.0782.0717.3
3.84.1899.610.0861.3777.5
3.533.899.810.1090.9527.6
3.323.5399.910.1490.6947.5
3.153.3210010.2050.5477.4
3.023.1597.810.2590.4866.1
2.93.0279.610.2610.5165.3
2.82.967.510.3070.4844.8
ReflectionResolution: 2.8→50 Å / Num. all: 20365 / Num. obs: 20365 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rsym value: 0.072 / Net I/σ(I): 25.43
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.98 / Num. unique all: 1424 / Rsym value: 0.307 / % possible all: 67.5

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
CNSrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→45 Å / FOM work R set: 0.758 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1998 9.3 %random
Rwork0.228 ---
all-20365 --
obs-20325 94.4 %-
Solvent computationBsol: 84.614 Å2
Displacement parametersBiso mean: 98.874 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 0 15 4307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.336
X-RAY DIFFRACTIONc_dihedral_angle_d19.801
X-RAY DIFFRACTIONc_improper_angle_d0.7775
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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