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- PDB-3t79: Ndc10: a platform for inner kinetochore assembly in budding yeast -

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Basic information

Entry
Database: PDB / ID: 3t79
TitleNdc10: a platform for inner kinetochore assembly in budding yeast
Components
  • DNA (5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*T)-3')
  • DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')
  • DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')
  • KLLA0E03807p
KeywordsDNA BINDING PROTEIN/DNA / DNA recombinase / DNA binding / DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA polymerase; domain 1 - #540 / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / 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 / hpI Integrase; Chain A / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / KLLA0E03807p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6113 Å
AuthorsCho, U.S. / Harrison, S.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Ndc10 is a platform for inner kinetochore assembly in budding yeast.
Authors: Cho, U.S. / Harrison, S.C.
History
DepositionJul 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jan 18, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')
C: DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)-3')
E: DNA (5'-D(P*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*T)-3')
A: KLLA0E03807p
D: KLLA0E03807p


Theoretical massNumber of molelcules
Total (without water)111,2686
Polymers111,2686
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')
C: DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)-3')
A: KLLA0E03807p


Theoretical massNumber of molelcules
Total (without water)55,7813
Polymers55,7813
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-14 kcal/mol
Surface area23370 Å2
MethodPISA
3
E: DNA (5'-D(P*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')
F: DNA (5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*T)-3')
D: KLLA0E03807p


Theoretical massNumber of molelcules
Total (without water)55,4863
Polymers55,4863
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-18 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.060, 99.651, 125.915
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: DNA chain DNA (5'-D(P*TP*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')


Mass: 4581.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA
#2: DNA chain DNA (5'-D(P*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*TP*TP*A)-3')


Mass: 4590.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA
#3: DNA chain DNA (5'-D(P*TP*AP*AP*TP*TP*TP*AP*TP*AP*AP*AP*AP*TP*T)-3')


Mass: 4276.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA
#4: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*TP*TP*TP*TP*AP*TP*AP*AP*AP*T)-3')


Mass: 4599.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized DNA
#5: Protein KLLA0E03807p


Mass: 46610.270 Da / Num. of mol.: 2 / Fragment: DNA binding domain (residues 1-402)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0E03807g / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CPM4

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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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 10,000, 0.1 M Tris-HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2010 / Details: MIRRORS
RadiationMonochromator: CHOZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. all: 13976 / Num. obs: 13821 / % possible obs: 99 % / Observed criterion σ(I): 22.4 / Redundancy: 3.4 % / Biso Wilson estimate: 67.92 Å2 / Rmerge(I) obs: 0.223 / Net I/σ(I): 1.4
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1374 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SQI

3sqi


Resolution: 3.6113→43.645 Å / SU ML: 0.98 / σ(F): 1.34 / Phase error: 36.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3309 686 4.98 %RANDOM
Rwork0.2864 ---
obs0.2885 13773 98.65 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.934 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso mean: 89.63 Å2
Baniso -1Baniso -2Baniso -3
1-29.6388 Å2-0 Å20 Å2
2---59.6494 Å20 Å2
3---23.6294 Å2
Refinement stepCycle: LAST / Resolution: 3.6113→43.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6392 1211 0 0 7603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097930
X-RAY DIFFRACTIONf_angle_d1.46611029
X-RAY DIFFRACTIONf_dihedral_angle_d21.7593004
X-RAY DIFFRACTIONf_chiral_restr0.0841234
X-RAY DIFFRACTIONf_plane_restr0.0071183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6113-3.890.38431380.38172561X-RAY DIFFRACTION99
3.89-4.28110.3551360.30062588X-RAY DIFFRACTION99
4.2811-4.89990.30221300.27672620X-RAY DIFFRACTION99
4.8999-6.17060.3731300.30082626X-RAY DIFFRACTION99
6.1706-43.64850.30061520.24732692X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3012-0.2970.28640.7495-0.6357-0.01560.1757-0.22150.1237-0.23860.03140.0877-0.2567-0.0564-01.0129-0.047-0.14770.7689-0.13360.551-36.1201-14.0622-48.4529
20.05531.16450.0651.19210.26651.0285-0.04580.19750.2865-0.52760.04370.08650.1062-0.2045-00.42080.0755-0.10840.6418-0.00480.6296-24.421814.2893-24.4512
30.4840.02070.30310.0976-0.02070.4150.18080.40130.1147-1.6852-0.4098-0.07240.08550.214700.738-0.064-0.38040.6978-0.01130.8316-66.526618.811-28.6743
4-0.36520.7636-0.350.5422-1.2267-0.28870.03880.2383-0.2365-0.4476-0.10020.68470.1671-0.0967-00.7762-0.005-0.05120.6845-0.05450.5922-49.4454-9.6198-8.3811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:100)
2X-RAY DIFFRACTION2chain 'A' and (resseq 101:402)
3X-RAY DIFFRACTION3chain 'D' and (resseq 1:100)
4X-RAY DIFFRACTION4chain 'D' and (resseq 101:402)

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