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- PDB-4aco: Structure of the budding yeast Ndc10 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4aco
TitleStructure of the budding yeast Ndc10 N-terminal domain
ComponentsCENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT A
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


CBF3 complex / septin ring assembly / mitotic spindle elongation / centromeric DNA binding / kinetochore assembly / condensed chromosome, centromeric region / spindle pole body / DNA binding, bending / spindle midzone / chromosome segregation ...CBF3 complex / septin ring assembly / mitotic spindle elongation / centromeric DNA binding / kinetochore assembly / condensed chromosome, centromeric region / spindle pole body / DNA binding, bending / spindle midzone / chromosome segregation / kinetochore / spindle / DNA binding / nucleus / cytoplasm
Similarity search - Function
Centromere DNA-binding protein complex CBF3 subunit, domain 2 / : / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A ...Centromere DNA-binding protein complex CBF3 subunit, domain 2 / : / Ndc10 N-terminal domain / Transcription activator GCR1-like domain / Ndc10, domain 2 / Ndc10, domain 2 superfamily / Transcriptional activator of glycolytic enzymes / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Integrase/recombinase, N-terminal / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centromere DNA-binding protein complex CBF3 subunit A
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.89 Å
AuthorsPerriches, T. / Singleton, M.R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Structure of the Yeast Kinetochore Ndc10 DNA-Binding Domain Reveals an Unexpected Evolutionary Relationship to Tyrosine Recombinases.
Authors: Perriches, T. / Singleton, M.R.
History
DepositionDec 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 29, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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 A


Theoretical massNumber of molelcules
Total (without water)112,0661
Polymers112,0661
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.740, 87.760, 104.570
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 CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT A / CENTROMERE-BINDING FACTOR 2 / CHROMOSOME TRANSMISSION FIDELITY PROTEIN 14 / KINETOCHORE PROTEIN CTF14 / NDC10


Mass: 112066.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P32504
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.36 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.89→67.22 Å / Num. obs: 39129 / % possible obs: 98.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.4

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.89→67.22 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.147 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23159 2054 5 %RANDOM
Rwork0.19253 ---
obs0.19443 39129 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.49 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.89→67.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 0 86 3879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023908
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9585297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20824.129201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13615666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8241518
X-RAY DIFFRACTIONr_chiral_restr0.1510.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213008
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 157 -
Rwork0.29 2637 -
obs--98.41 %

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