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- PDB-6lbr: Crystal structure of yeast Cdc13 and ssDNA -

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Basic information

Entry
Database: PDB / ID: 6lbr
TitleCrystal structure of yeast Cdc13 and ssDNA
Components
  • KLLA0F20922p
  • Telomere single-strand DNA
KeywordsDNA BINDING PROTEIN/DNA / Telomere / Protein-ssDNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


telomere maintenance / chromosome, telomeric region / DNA binding
Similarity search - Function
Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus / Cdc13 OB4 dimerization domain / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / KLLA0F20922p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsGe, Y. / Wu, Z. / Wu, J. / Lei, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: Structural insights into telomere protection and homeostasis regulation by yeast CST complex.
Authors: Ge, Y. / Wu, Z. / Chen, H. / Zhong, Q. / Shi, S. / Li, G. / Wu, J. / Lei, M.
History
DepositionNov 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 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: KLLA0F20922p
B: KLLA0F20922p
C: Telomere single-strand DNA
D: Telomere single-strand DNA


Theoretical massNumber of molelcules
Total (without water)141,8644
Polymers141,8644
Non-polymers00
Water4,089227
1
A: KLLA0F20922p
C: Telomere single-strand DNA


Theoretical massNumber of molelcules
Total (without water)70,9322
Polymers70,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-15 kcal/mol
Surface area27880 Å2
MethodPISA
2
B: KLLA0F20922p
D: Telomere single-strand DNA


Theoretical massNumber of molelcules
Total (without water)70,9322
Polymers70,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-13 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.166, 106.955, 173.521
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KLLA0F20922p / Cdc13


Mass: 63116.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Cell line (production host): High Five / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6CJ70
#2: DNA chain Telomere single-strand DNA


Mass: 7815.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Kluyveromyces lactis (yeast)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 25% Ethylene Glycol, 0.01 mM EDTA and 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 49182 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.05 / Rrim(I) all: 0.115 / Χ2: 0.954 / Net I/σ(I): 5.9 / Num. measured all: 270829
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.595.70.84348430.7690.3790.9270.91499.8
2.59-2.695.50.58448300.8620.2660.6430.91599.7
2.69-2.825.20.41448480.910.1960.4590.93799.8
2.82-2.965.50.29848620.9490.1370.3290.936100
2.96-3.155.70.20948830.970.0950.230.97699.9
3.15-3.395.70.14348790.980.0660.1580.97499.9
3.39-3.735.30.10549130.9840.0510.1170.98899.9
3.73-4.275.70.09149430.9880.0420.11.013100
4.27-5.385.40.08149910.9870.0390.0910.95699.7
5.38-505.30.07551900.990.0380.0840.92499.7

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-3000data collection
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→45.84 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2518 2217 4.8 %
Rwork0.2017 --
obs0.2041 46144 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.46 Å2 / Biso mean: 44.3735 Å2 / Biso min: 12.2 Å2
Refinement stepCycle: final / Resolution: 2.5→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 940 0 227 7028
Biso mean---43.46 -
Num. residues----772
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.55450.2992860.2538151352
2.5545-2.61390.3144970.2466199669
2.6139-2.67930.27531220.2348250587
2.6793-2.75170.3061360.2417276396
2.7517-2.83270.28051450.2359284099
2.8327-2.92410.3031620.2152859100
2.9241-3.02860.25111270.20942923100
3.0286-3.14980.26591400.20382919100
3.1498-3.29310.24781340.19412898100
3.2931-3.46670.26381550.19252890100
3.4667-3.68380.24971590.17882905100
3.6838-3.96810.24431530.17492945100
3.9681-4.36710.22671580.16582920100
4.3671-4.99840.20511450.16762954100
4.9984-6.29490.22421480.21642991100
6.2949-45.840.27381500.2507310699
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)
10.791.0293-0.27982.2532-0.68820.22650.01070.08250.0747-0.16750.04460.17110.0818-0.081-0.010.15050.0332-0.01420.20.00380.147355.07646.125125.262
21.6342-0.2309-0.19411.2394-0.13641.90160.0239-0.0108-0.02820.21720.02030.01840.21920.0993-0.01360.21550.01690.01110.306-0.05310.203848.48920.57167.019
31.46710.62880.02531.8933-0.39412.6967-0.08040.20610.31950.05760.03140.4093-0.1622-0.5348-0.1170.15290.02140.04160.26440.02970.393760.34375.737119.297
42.26480.1677-0.45821.5688-0.74322.2474-0.0375-0.205-0.62450.1311-0.1213-0.06690.31750.06010.00560.36470.0281-0.02440.3687-0.07070.430546.31514.511161.763
50.25150.0826-0.00360.1312-0.03880.2311-0.00830.02070.0828-0.02070.03870.09520.0113-0.0259-0.01680.17630.01780.01310.189-0.02740.23956.87143.392133.941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 369:897 )A369 - 897
2X-RAY DIFFRACTION2( CHAIN B AND RESID 506:717 )B506 - 717
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:22 )C1 - 22
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:23 )D1 - 23
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1001:1148 ) OR ( CHAIN C AND RESID 101:124 ) OR ( CHAIN B AND RESID 1001:1035 ) OR ( CHAIN D AND RESID 101:120 )A1001 - 1148
6X-RAY DIFFRACTION5( CHAIN A AND RESID 1001:1148 ) OR ( CHAIN C AND RESID 101:124 ) OR ( CHAIN B AND RESID 1001:1035 ) OR ( CHAIN D AND RESID 101:120 )C101 - 124
7X-RAY DIFFRACTION5( CHAIN A AND RESID 1001:1148 ) OR ( CHAIN C AND RESID 101:124 ) OR ( CHAIN B AND RESID 1001:1035 ) OR ( CHAIN D AND RESID 101:120 )B1001 - 1035
8X-RAY DIFFRACTION5( CHAIN A AND RESID 1001:1148 ) OR ( CHAIN C AND RESID 101:124 ) OR ( CHAIN B AND RESID 1001:1035 ) OR ( CHAIN D AND RESID 101:120 )D101 - 120

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