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- PDB-6lbu: Crystal structure of yeast Stn1 and Ten1 -

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Basic information

Entry
Database: PDB / ID: 6lbu
TitleCrystal structure of yeast Stn1 and Ten1
Components
  • KLLA0C11825p
  • KLLA0E09417p
KeywordsDNA BINDING PROTEIN / Telomere / CST complex
Function / homology
Function and homology information


CST complex / telomere capping
Similarity search - Function
Stn1, C-terminal, fungi / Stn1, C-terminal domain superfamily / Telomere capping C-terminal wHTH / CST complex subunit Stn1, N-terminal / Telomere regulation protein Stn1 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
KLLA0E09417p / KLLA0C11825p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KLLA0C11825p
B: KLLA0E09417p


Theoretical massNumber of molelcules
Total (without water)38,8262
Polymers38,8262
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-8 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.306, 78.031, 101.151
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 KLLA0C11825p / Stn1


Mass: 22276.131 Da / Num. of mol.: 1 / Mutation: C122M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CTL1
#2: Protein KLLA0E09417p / Ten1


Mass: 16550.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6CNW4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 0.2 M potassium chloride, 0.05 M Sodium cacodylate trihydrate, 10% (w/v) PEG4000

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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: Jan 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24869 / % possible obs: 99.5 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.026 / Rrim(I) all: 0.092 / Χ2: 0.729 / Net I/σ(I): 4.6 / Num. measured all: 314501
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0711.30.37223380.9790.110.3890.47695.7
2.07-2.1512.10.30624470.9890.0890.3190.4899.2
2.15-2.2512.80.26924450.9910.0770.280.599.8
2.25-2.3712.60.22224720.9930.0650.2320.505100
2.37-2.5213.60.18324810.9950.0510.190.535100
2.52-2.7113.10.1424520.9960.040.1450.572100
2.71-2.9912.70.10724970.9970.0310.1120.651100
2.99-3.4213.30.08124950.9980.0230.0850.803100
3.42-4.3112.80.06625440.9980.0190.0691.074100
4.31-5012.10.06226980.9990.0180.0641.602100

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→30.951 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.48
RfactorNum. reflection% reflection
Rfree0.2575 1209 4.89 %
Rwork0.2114 --
obs0.2135 24707 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.56 Å2 / Biso mean: 42.1632 Å2 / Biso min: 16.23 Å2
Refinement stepCycle: final / Resolution: 2→30.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2651 0 0 173 2824
Biso mean---48.75 -
Num. residues----320
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.08010.30341210.245242894
2.0801-2.17470.27111350.2308257199
2.1747-2.28940.28361380.22652551100
2.2894-2.43280.30331400.21882604100
2.4328-2.62050.25251350.20852612100
2.6205-2.8840.29791480.22082601100
2.884-3.3010.27171340.22182645100
3.301-4.15730.20271280.20112682100
4.1573-30.950.25421300.1995280499
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)
10.8152-0.70960.43713.1319-1.01321.50810.03840.0403-0.0423-0.20310.05070.29330.0651-0.1243-0.00520.1631-0.03730.0140.13470.00110.1274-29.3463.646-18.034
21.8901-1.68451.39023.3202-1.16392.9547-0.2158-0.2020.05670.7330.0806-0.0588-0.1906-0.18380.02350.32040.00090.01930.1873-0.00010.2432-11.778-2.6955.854
30.5727-0.72790.44241.5535-0.2250.92110.0677-0.0894-0.03570.0451-0.04490.0450.0277-0.10720.00590.4432-0.0470.06980.37020.01290.3543-22.3940.046-9.338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:190 )A2 - 190
2X-RAY DIFFRACTION2( CHAIN B AND RESID 0:140 )B0 - 140
3X-RAY DIFFRACTION3( CHAIN A AND RESID 201:317 ) OR ( CHAIN B AND RESID 201:256 )A201 - 317
4X-RAY DIFFRACTION3( CHAIN A AND RESID 201:317 ) OR ( CHAIN B AND RESID 201:256 )B201 - 256

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