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- PDB-6lbt: Crystal structure of yeast Cdc13 and Stn1 -

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Basic information

Entry
Database: PDB / ID: 6lbt
TitleCrystal structure of yeast Cdc13 and Stn1
Components
  • KLLA0C11825p
  • KLLA0F20922p,KLLA0F20922p
KeywordsDNA BINDING PROTEIN / Telomere / CST complex
Function / homology
Function and homology information


CST complex / telomere capping / telomere maintenance / chromosome, telomeric region / DNA binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #810 / Stn1, C-terminal wHTH domain / Stn1, C-terminal, fungi / Stn1, C-terminal domain superfamily / Telomere capping C-terminal wHTH / CST complex subunit Stn1, N-terminal / Telomere regulation protein Stn1 / Cell division control protein 13, N-terminal / Cdc13, OB4 dimerization domain / Cell division control protein 13 N-terminus ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #810 / Stn1, C-terminal wHTH domain / Stn1, C-terminal, fungi / Stn1, C-terminal domain superfamily / Telomere capping C-terminal wHTH / CST complex subunit Stn1, N-terminal / Telomere regulation protein Stn1 / 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 / Ribosomal Protein S8; Chain: A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
KLLA0F20922p / KLLA0C11825p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3Nov 22, 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
A: KLLA0F20922p,KLLA0F20922p
C: KLLA0C11825p
B: KLLA0F20922p,KLLA0F20922p
D: KLLA0C11825p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0335
Polymers111,9414
Non-polymers921
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-14 kcal/mol
Surface area44400 Å2
Unit cell
Length a, b, c (Å)74.971, 84.577, 165.393
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,KLLA0F20922p / Cdc13


Mass: 36577.703 Da / Num. of mol.: 2
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: Q6CJ70
#2: Protein KLLA0C11825p / Stn1


Mass: 19392.840 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7 / Details: 0.225 M ammonium citrate tribasic, 12% PEG3350

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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: Nov 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33308 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.035 / Rrim(I) all: 0.124 / Χ2: 0.742 / Net I/σ(I): 4.1 / Num. measured all: 428976
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6912.70.86332710.9010.2490.8990.451100
2.69-2.813.30.70132520.940.1980.7290.462100
2.8-2.9313.20.52732930.9690.150.5480.477100
2.93-3.0812.70.36832840.9820.1070.3830.521100
3.08-3.2812.50.25433030.9890.0740.2650.575100
3.28-3.5313.50.18333090.9940.0510.190.666100
3.53-3.8813.20.12833210.9960.0360.1330.829100
3.88-4.4512.60.09533470.9970.0280.0991.009100
4.45-5.613.20.0833700.9970.0230.0841.132100
5.6-5011.90.07335580.9980.0230.0771.28799.9

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
HKL-3000data collection
HKL-3000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LBR, 6LBS

6lbr

6lbs


Resolution: 2.6→36.207 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.88
RfactorNum. reflection% reflection
Rfree0.2579 1624 4.92 %
Rwork0.2165 --
obs0.2185 33028 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.03 Å2 / Biso mean: 62.5444 Å2 / Biso min: 29.23 Å2
Refinement stepCycle: final / Resolution: 2.6→36.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7341 0 6 15 7362
Biso mean--58.35 49.53 -
Num. residues----900
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.67650.33751360.32762573100
2.6765-2.76280.34961530.31562544100
2.7628-2.86160.33261310.282588100
2.8616-2.97610.32991340.28132591100
2.9761-3.11150.3031370.27892574100
3.1115-3.27540.39461550.2752580100
3.2754-3.48050.26091320.22582583100
3.4805-3.74890.26351320.21752637100
3.7489-4.12570.25571300.20962628100
4.1257-4.72160.21461310.17182659100
4.7216-5.94450.20711340.17992664100
5.9445-36.20.20711190.1937278398
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)
10.5407-0.1756-0.51550.7696-0.34162.0231-0.01060.0788-0.00620.02940.0347-0.02340.01620.0567-00.29-0.00420.0060.2973-0.02110.3486-11.7827.964-41.452
20.4445-0.1217-0.08380.8743-0.58741.3309-0.0121-0.1227-0.0366-0.1728-0.0076-0.00360.03150.166200.3708-0.0102-0.01520.40390.05430.3569-19.2332.0111.831
30.8206-0.10980.33991.0064-0.33241.6107-0.0049-0.0770.09560.08660.1008-0.10760.0118-0.023-00.36490.02610.01680.3486-0.03980.3885-13.43135.3349.299
40.41450.4567-0.5440.8276-0.12380.9746-0.0209-0.028-0.0466-0.0331-0.06580.0433-0.0090.0468-00.39070.06090.01930.37580.05950.367-23.56639.902-33.496
52.00071.99951.99962.00042.000520.19140.41730.6468-0.25690.15630.5502-6.22391.5187-0.28240.51430.05840.27960.82110.19070.58883.222.743-30.501
6-0.2229-0.1315-0.14320.1523-0.2353-0.0978-0.12790.1381-0.01740.09360.07330.1345-0.2324-0.02800.2336-0.08240.10480.4250.09030.5449-16.2432.551-1.532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 374:891 )A374 - 891
2X-RAY DIFFRACTION2( CHAIN C AND RESID 274:434 )C274 - 434
3X-RAY DIFFRACTION3( CHAIN B AND RESID 374:892 )B374 - 892
4X-RAY DIFFRACTION4( CHAIN D AND RESID 274:434 )D274 - 434
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1001:1001 )A1001
6X-RAY DIFFRACTION6( CHAIN A AND RESID 1101:1102 ) OR ( CHAIN C AND RESID 501:502 ) OR ( CHAIN B AND RESID 1001:1008 ) OR ( CHAIN D AND RESID 501:503 )A1101 - 1102
7X-RAY DIFFRACTION6( CHAIN A AND RESID 1101:1102 ) OR ( CHAIN C AND RESID 501:502 ) OR ( CHAIN B AND RESID 1001:1008 ) OR ( CHAIN D AND RESID 501:503 )C501 - 502
8X-RAY DIFFRACTION6( CHAIN A AND RESID 1101:1102 ) OR ( CHAIN C AND RESID 501:502 ) OR ( CHAIN B AND RESID 1001:1008 ) OR ( CHAIN D AND RESID 501:503 )B1001 - 1008
9X-RAY DIFFRACTION6( CHAIN A AND RESID 1101:1102 ) OR ( CHAIN C AND RESID 501:502 ) OR ( CHAIN B AND RESID 1001:1008 ) OR ( CHAIN D AND RESID 501:503 )D501 - 503

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