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- PDB-2veq: Insights into kinetochore-DNA interactions from the structure of Cep3p -

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Basic information

Entry
Database: PDB / ID: 2veq
TitleInsights into kinetochore-DNA interactions from the structure of Cep3p
ComponentsCENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT B
KeywordsCELL CYCLE / TRANSCRIPTION FACTOR / ZINC / CEP3P / NUCLEUS / CENTROMERE / DNA-BINDING / PHOSPHORYLATION / CHROMOSOMAL PROTEIN / KINETOCHORE / CBF3 COMPLEX / METAL-BINDING
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
BETA-MERCAPTOETHANOL / CACODYLATE ION / Centromere DNA-binding protein complex CBF3 subunit B
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.49 Å
AuthorsPurvis, A. / Singleton, M.R.
CitationJournal: Embo Rep. / Year: 2008
Title: Insights Into Kinetochore-DNA Interactions from the Structure of Cep3Delta
Authors: Purvis, A. / Singleton, M.R.
History
DepositionOct 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5943
Polymers66,3791
Non-polymers2152
Water1,40578
1
A: CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT B
hetero molecules

A: CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,1886
Polymers132,7582
Non-polymers4304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7380 Å2
ΔGint-60.4 kcal/mol
Surface area52580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)83.737, 83.737, 231.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT B / CENTROMERE PROTEIN 3 / CEP3P


Mass: 66378.820 Da / Num. of mol.: 1 / Fragment: RESIDUES 48-608
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P40969
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details2-MERCAPTOETHANOL (BME): COVALENTLY ATTACHED TO CYS A297
Sequence detailsTRUNCATED CEP3P RESIDUES 48-608 THE TRUNCATED PROTEIN IS NUMBERED ACCORDING TO THE FULL LENGTH ...TRUNCATED CEP3P RESIDUES 48-608 THE TRUNCATED PROTEIN IS NUMBERED ACCORDING TO THE FULL LENGTH CEP3P SEQUENCE. DISULPHIDE LINK IS PRESENT BETWEEN A99 AND A215. DISORDERED REGIONS (N-TERMINUS-A48, A314- A335, A570-A587) WERE OMITTED FROM THE STRUCTURE. DISORDERED SIDE CHAINS OF UNDETERMINED ORIENTATION WERE GIVEN ZERO OCCUPANCY (65 ATOMS IN TOTAL)

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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: 3.29 Å3/Da / Density % sol: 59.8 %
Description: SAD DATA COLLECTED FROM SELENOMETHIONINE- SUBSTITUTED PROTEIN
Crystal growpH: 6.5
Details: 100MM SODIUM CACODYLATE PH 6.5, 0.2M POTASSIUM THIOCYANATE, 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2007 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: SI(311) AND SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→41.9 Å / Num. obs: 29594 / % possible obs: 99.6 % / Redundancy: 7.7 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.49→41.2 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2285567.38 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES N-TERMINUS-A48, A314- - A335, AND A570-A587 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1484 5 %RANDOM
Rwork0.22 ---
obs0.22 29522 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8661 Å2 / ksol: 0.323757 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.96 Å20 Å20 Å2
2--4.96 Å20 Å2
3----9.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.49→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4318 0 9 78 4405
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.851.5
X-RAY DIFFRACTIONc_mcangle_it2.932
X-RAY DIFFRACTIONc_scbond_it5.642
X-RAY DIFFRACTIONc_scangle_it6.842.5
LS refinement shellResolution: 2.49→2.65 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 248 5.2 %
Rwork0.261 4502 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PRODRG_BME_MODIFIED.PARPRODRG_BME_MODIFIED.TOP
X-RAY DIFFRACTION4PRODRG_CAC_MODIFIED.PARPRODRG_CAC_MODIFIED.TOP

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