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- PDB-6lbs: Crystal structure of yeast Stn1 -

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Basic information

Entry
Database: PDB / ID: 6lbs
TitleCrystal structure of yeast Stn1
ComponentsKLLA0C11825p
KeywordsDNA BINDING PROTEIN / Telomere / CST complex
Function / homology
Function and homology information


CST complex / telomere capping
Similarity search - Function
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 / Ribosomal Protein S8; Chain: A, domain 1 / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 1.3Oct 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: KLLA0C11825p
C: KLLA0C11825p
D: KLLA0C11825p
E: KLLA0C11825p
F: KLLA0C11825p


Theoretical massNumber of molelcules
Total (without water)117,7646
Polymers117,7646
Non-polymers00
Water2,270126
1
A: KLLA0C11825p


Theoretical massNumber of molelcules
Total (without water)19,6271
Polymers19,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KLLA0C11825p


Theoretical massNumber of molelcules
Total (without water)19,6271
Polymers19,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: KLLA0C11825p


Theoretical massNumber of molelcules
Total (without water)19,6271
Polymers19,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: KLLA0C11825p


Theoretical massNumber of molelcules
Total (without water)19,6271
Polymers19,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: KLLA0C11825p


Theoretical massNumber of molelcules
Total (without water)19,6271
Polymers19,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: KLLA0C11825p


Theoretical massNumber of molelcules
Total (without water)19,6271
Polymers19,6271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.425, 94.749, 97.498
Angle α, β, γ (deg.)90.000, 96.260, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
KLLA0C11825p / Stn1


Mass: 19627.316 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 3.09 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 4 / Details: 0.1 M citric acid, 0.8 M ammonium sulfate

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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: Apr 17, 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: 84248 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.029 / Rrim(I) all: 0.075 / Χ2: 0.84 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.696.80.72244460.8080.30.7830.927100
2.69-2.86.40.51544750.8840.2220.5620.911100
2.8-2.936.80.39644120.9250.1630.4290.938100
2.93-3.087.10.26444630.9620.1070.2860.90399.9
3.08-3.2870.16444660.9850.0670.1770.93100
3.28-3.536.80.09844640.9910.040.1060.8999.9
3.53-3.886.60.06244740.9950.0260.0680.82100
3.88-4.457.20.04644550.9970.0180.0490.80699.8
4.45-5.66.60.03644890.9970.0150.0390.66399.9
5.6-506.90.03145720.9970.0130.0330.61699.9

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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: 2.6→37.946 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 24.73
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2349 4111 4.88 %
Rwork0.1832 --
obs0.1857 84248 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.74 Å2 / Biso mean: 46.0584 Å2 / Biso min: 15.11 Å2
Refinement stepCycle: final / Resolution: 2.6→37.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7337 0 0 126 7463
Biso mean---39.93 -
Num. residues----884
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.63060.35031340.2559211174
2.6306-2.66270.37891430.2458226281
2.6627-2.69640.26191420.2395237485
2.6964-2.73180.27721230.2211263693
2.7318-2.76920.33251480.2336266094
2.7692-2.80880.26661400.2302280198
2.8088-2.85070.2851380.239285599
2.8507-2.89520.25911220.23772838100
2.8952-2.94270.32241580.23982812100
2.9427-2.99340.32241690.24622816100
2.9934-3.04780.31651340.23272916100
3.0478-3.10640.31961250.22272779100
3.1064-3.16980.25241500.21612855100
3.1698-3.23870.26961150.21382893100
3.2387-3.3140.27871080.21442870100
3.314-3.39680.25731350.2032864100
3.3968-3.48860.27681570.18842812100
3.4886-3.59120.22651530.17072818100
3.5912-3.7070.20711330.17222865100
3.707-3.83930.21891350.16462857100
3.8393-3.99290.22361720.16152824100
3.9929-4.17440.17531510.1422815100
4.1744-4.39420.16511450.1352878100
4.3942-4.6690.17921390.13162819100
4.669-5.02880.17071300.13662841100
5.0288-5.53350.20221540.15022822100
5.5335-6.3310.23491690.1942835100
6.331-7.96420.26451650.20832816100
7.9642-37.940.17611240.1581279398
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)
12.32141.1566-0.38391.4587-0.48271.2780.30280.0739-0.13960.1063-0.2765-0.19680.17920.2866-0.00020.28480.0851-0.06020.3317-0.05680.1974-101.52656.07242.644
21.2710.4229-0.13282.229-0.95281.0191-0.0996-0.1232-0.11240.0136-0.005-0.3108-0.0174-0.0008-0.00010.31050.0624-0.01020.19680.00860.3173-119.37316.34740.746
31.71481.27760.13622.0897-1.11571.3547-0.0586-0.19990.06250.18270.13660.11-0.33850.22770.00310.27380.06750.0710.3514-0.0420.2434-99.787-12.32925.34
42.12650.38010.62270.6733-0.57070.7717-0.0545-0.05360.11210.01120.06430.0580.00540.0207-00.26080.01870.01030.2119-0.08530.1757-55.371-11.90121.539
50.23710.3711-0.37632.35030.43481.7036-0.05260.13890.01870.0528-0.10090.03030.0652-0.3878-0.00190.2061-0.03340.01820.2636-0.04080.2526-39.52918.0228.868
62.1874-1.27330.07531.61360.17180.9174-0.0318-0.0989-0.1255-0.04010.00020.00550.0745-0.092-0.00010.1506-0.01020.00070.2061-0.03120.2259-63.75755.1237.985
7-0.17-0.1728-0.04330.1474-0.1336-0.2748-0.09560.10260.1327-0.04110.077-0.0283-0.03670.0578-0.00240.34330.049-0.0150.1507-0.14080.1281-68.82124.27820.562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 274:432 )A274 - 432
2X-RAY DIFFRACTION2( CHAIN B AND RESID 274:433 )B274 - 433
3X-RAY DIFFRACTION3( CHAIN C AND RESID 274:430 )C274 - 430
4X-RAY DIFFRACTION4( CHAIN D AND RESID 273:433 )D273 - 433
5X-RAY DIFFRACTION5( CHAIN E AND RESID 275:433 )E275 - 433
6X-RAY DIFFRACTION6( CHAIN F AND RESID 274:433 )F274 - 433
7X-RAY DIFFRACTION7( CHAIN A AND RESID 501:513 ) OR ( CHAIN C AND RESID 501:510 ) OR ( CHAIN B AND RESID 501:513 ) OR ( CHAIN E AND RESID 501:525 ) OR ( CHAIN D AND RESID 501:529 ) OR ( CHAIN F AND RESID 501:536 )A501 - 513
8X-RAY DIFFRACTION7( CHAIN A AND RESID 501:513 ) OR ( CHAIN C AND RESID 501:510 ) OR ( CHAIN B AND RESID 501:513 ) OR ( CHAIN E AND RESID 501:525 ) OR ( CHAIN D AND RESID 501:529 ) OR ( CHAIN F AND RESID 501:536 )C501 - 510
9X-RAY DIFFRACTION7( CHAIN A AND RESID 501:513 ) OR ( CHAIN C AND RESID 501:510 ) OR ( CHAIN B AND RESID 501:513 ) OR ( CHAIN E AND RESID 501:525 ) OR ( CHAIN D AND RESID 501:529 ) OR ( CHAIN F AND RESID 501:536 )B501 - 513
10X-RAY DIFFRACTION7( CHAIN A AND RESID 501:513 ) OR ( CHAIN C AND RESID 501:510 ) OR ( CHAIN B AND RESID 501:513 ) OR ( CHAIN E AND RESID 501:525 ) OR ( CHAIN D AND RESID 501:529 ) OR ( CHAIN F AND RESID 501:536 )E501 - 525
11X-RAY DIFFRACTION7( CHAIN A AND RESID 501:513 ) OR ( CHAIN C AND RESID 501:510 ) OR ( CHAIN B AND RESID 501:513 ) OR ( CHAIN E AND RESID 501:525 ) OR ( CHAIN D AND RESID 501:529 ) OR ( CHAIN F AND RESID 501:536 )D501 - 529
12X-RAY DIFFRACTION7( CHAIN A AND RESID 501:513 ) OR ( CHAIN C AND RESID 501:510 ) OR ( CHAIN B AND RESID 501:513 ) OR ( CHAIN E AND RESID 501:525 ) OR ( CHAIN D AND RESID 501:529 ) OR ( CHAIN F AND RESID 501:536 )F501 - 536

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