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- PDB-3sqi: DNA binding domain of Ndc10 -

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Basic information

Entry
Database: PDB / ID: 3sqi
TitleDNA binding domain of Ndc10
Components
  • 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*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 / SAD / Resolution: 2.8245 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 5, 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 1.3Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: KLLA0E03807p
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')


Theoretical massNumber of molelcules
Total (without water)70,6823
Polymers70,6823
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-17 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.303, 147.536, 95.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein KLLA0E03807p


Mass: 61510.867 Da / Num. of mol.: 1 / Fragment: DNA binding domain (residues 1-534)
Source method: isolated from a genetically manipulated source
Details: ligation independent cloning (LIC) / Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: NRRL Y-1140 / Gene: KLLA0E03807g / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6CPM4
#2: 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: Synthetic construct
#3: 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: Synthetic construct

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG400, 0.1 M MES pH 6.0, 0.2 M NaCl, 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: Jun 12, 2009
RadiationMonochromator: the Phase 2 monochromator using Si (220) crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 20316 / Num. obs: 18620 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 14.7 % / Biso Wilson estimate: 78.9 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.083 / Net I/σ(I): 23.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2 / Rsym value: 0.626 / % possible all: 74.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8245→41.388 Å / SU ML: 0.71 / σ(F): 1.34 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 954 5.14 %
Rwork0.1934 --
obs0.1962 18554 91.44 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.183 Å2 / ksol: 0.292 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-47.59 Å2-0 Å2-0 Å2
2---15.5982 Å2-0 Å2
3----31.9918 Å2
Refinement stepCycle: LAST / Resolution: 2.8245→41.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 615 0 0 3811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053975
X-RAY DIFFRACTIONf_angle_d1.1475530
X-RAY DIFFRACTIONf_dihedral_angle_d20.7361507
X-RAY DIFFRACTIONf_chiral_restr0.071619
X-RAY DIFFRACTIONf_plane_restr0.004592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8245-2.97330.3883950.2991947X-RAY DIFFRACTION71
2.9733-3.15960.34621240.27692226X-RAY DIFFRACTION83
3.1596-3.40340.311480.25652404X-RAY DIFFRACTION89
3.4034-3.74570.29681660.21532674X-RAY DIFFRACTION98
3.7457-4.28720.23081490.16472722X-RAY DIFFRACTION100
4.2872-5.39960.2111280.15962772X-RAY DIFFRACTION100
5.3996-41.39210.22131440.18222855X-RAY DIFFRACTION99
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)
17.4586-0.17821.47248.02714.02422.9909-1.00870.3681.528-0.89340.52530.1499-3.22120.10310.52941.36470.1507-0.20840.73760.18930.901912.265214.2658-43.7579
26.3526-1.98350.00618.8409-2.50855.7279-0.52650.17411.1808-0.23310.2329-0.6216-1.39840.87140.21351.1127-0.1548-0.1490.65990.08520.473515.65844.9022-34.6502
36.22112.79-0.47842.47270.1727.563-0.0051-0.2054-0.64570.09680.05880.08222.45150.80120.05251.00530.48910.15780.3667-0.12540.6511.664-27.768-16.1735
41.8253-0.5105-0.92187.7683-2.5787.2558-0.03790.2850.35220.2961-0.1648-0.55740.09840.87430.10610.26550.19180.03180.5392-0.05790.535117.3205-13.5118-11.2116
53.6626-2.80942.20264.0166-2.01697.9645-0.26710.16970.10250.4717-0.0622-0.44841.1031.50570.30330.80570.3416-0.04940.84570.00140.388720.2668-20.1033-15.6087
65.50592.9537-3.52365.9574-1.38595.09330.1319-1.05180.1151.24350.0520.25680.25590.4397-0.20940.97320.27510.04680.6157-0.06120.53739.7834-18.02960.8064
75.4729-3.1485-4.24442.76433.3556.938-1.18980.2972-0.98121.25930.21941.16192.2548-0.64231.08972.2733-0.0401-0.12220.8651-0.06661.0283-3.2631-27.6013-9.0862
82.50790.91751.6281.35231.18415.87420.22830.3616-0.80240.12720.08390.13690.37342.22680.03942.20570.86640.0641.85020.00040.601832.0447-37.5917-26.3093
94.76131.83611.1865.69713.43672.68290.40670.5196-0.2952-1.0087-0.2365-0.20972.21622.00980.25562.15490.9510.21561.61720.09570.706930.5415-39.2483-21.8304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:31)
2X-RAY DIFFRACTION2chain 'A' and (resseq 32:100)
3X-RAY DIFFRACTION3chain 'A' and (resseq 101:149)
4X-RAY DIFFRACTION4chain 'A' and (resseq 150:210)
5X-RAY DIFFRACTION5chain 'A' and (resseq 211:310)
6X-RAY DIFFRACTION6chain 'A' and (resseq 311:376)
7X-RAY DIFFRACTION7chain 'A' and (resseq 377:402)
8X-RAY DIFFRACTION8chain 'B'
9X-RAY DIFFRACTION9chain 'C'

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