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- PDB-3k10: Crystal structure of telomere capping protein Stn1 from Saccharom... -

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Basic information

Entry
Database: PDB / ID: 3k10
TitleCrystal structure of telomere capping protein Stn1 from Saccharomyces cerevisiae
ComponentsProtein STN1
KeywordsPROTEIN BINDING / winged helix turn helix / telomere capping / Chromosomal protein / Phosphoprotein / Telomere
Function / homology
Function and homology information


CST complex / translation elongation factor binding / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / telomere capping / negative regulation of telomere maintenance via telomerase / chromosome, telomeric region
Similarity search - Function
Stn1, N-terminal wHTH domain / 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 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich ...Stn1, N-terminal wHTH domain / 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 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsGelinas, A.D. / Reyes, F.E. / Batey, R.T. / Wuttke, D.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Telomere capping proteins are structurally related to RPA with an additional telomere-specific domain.
Authors: Gelinas, A.D. / Paschini, M. / Reyes, F.E. / Heroux, A. / Batey, R.T. / Lundblad, V. / Wuttke, D.S.
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein STN1


Theoretical massNumber of molelcules
Total (without water)20,5571
Polymers20,5571
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.709, 52.709, 186.552
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein STN1


Mass: 20556.893 Da / Num. of mol.: 1 / Fragment: UNP residues 313-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: D4456, STN1, YD8554.15, YDR082W / Plasmid: pET duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38960
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1560.97
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2901vapor diffusion, hanging drop8.415% w/v PEG 1000, 10 mM EDTA, 0.1 M Tris-HCl pH 8.4, 10mM PtCl4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
2902vapor diffusion, hanging drop8.415% w/v PEG 1000, 10 mM EDTA, 0.1 M Tris-HCl pH 8.4, 6mM KAuCl4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
193.151
293.151
393.151
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.502
ROTATING ANODERIGAKU21.502
SYNCHROTRONNSLS X29A31.0809
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEAug 4, 2008
RIGAKU RAXIS IV2IMAGE PLATEAug 4, 2008
ADSC QUANTUM 315r3CCDJun 19, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.5021
21.08091
Reflection

Av σ(I) over netI: 34.78

Redundancy (%)IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)Num. obs% possible obs
3.831391060.0810.97346.011001298.7
3.262544260.1220.962.5345.961655798.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancyRejects
6.4646.019710.0310.933.75249
5.136.4699.510.0650.953.8947
4.485.1399.410.0530.923.8740
4.074.489910.0660.963.8558
3.784.079910.0890.963.8440
3.563.789910.1150.983.8261
3.383.5698.910.1470.963.8360
3.233.3898.510.1810.993.8461
3.113.2398.510.21413.7873
33.1198.310.2381.093.8195
5.4545.9698.620.0430.853.85211
4.335.4599.920.0740.843.8740
3.784.3399.920.1140.913.8434
3.433.7899.920.1720.933.8337
3.193.4399.920.2391.043.838
33.1910020.2881.053.831
2.85310020.3251.113.613
2.732.8599.920.3131.032.463
2.622.7396.720.3081.021.832
2.532.628920.2870.841.48
ReflectionResolution: 2.3→50 Å / Num. obs: 13389 / % possible obs: 85.5 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.063 / Χ2: 1.494 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.384.60.4214291.02635.5
2.38-2.487.80.4316711.1455.5
2.48-2.597.80.4238722.04771.9
2.59-2.737.70.34510911.70389.4
2.73-2.98.40.26612131.40498.1
2.9-3.128.80.15712331.26299.8
3.12-3.449.10.10212271.42699.8
3.44-3.9390.06412671.72999.8
3.93-4.959.40.0412881.54199.9
4.95-509.70.03214191.35999.9

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Phasing

PhasingMethod: SIRAS
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
111.8660.65212.579AU600.52
210.8620.23115.697AU55.80.41
318.85314.4963.652AU600.2
Phasing dmFOM : 0.77 / FOM acentric: 0.77 / FOM centric: 0.76 / Reflection: 5170 / Reflection acentric: 3855 / Reflection centric: 1315
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.9-40.3250.820.910.74246114132
5.5-8.90.830.860.77741479262
4.4-5.50.850.860.82872631241
3.9-4.40.810.820.81881676205
3.3-3.90.740.740.7615171212305
3.1-3.30.610.610.63913743170

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.742 / σ(F): 1480
RfactorNum. reflection% reflection
Rfree0.301 1406 7.4 %
Rwork0.246 --
obs-10710 77.3 %
Solvent computationBsol: 47.133 Å2
Displacement parametersBiso max: 114.95 Å2 / Biso mean: 55.273 Å2 / Biso min: 30.75 Å2
Baniso -1Baniso -2Baniso -3
1-10.923 Å2-0 Å20 Å2
2--10.923 Å20 Å2
3----21.846 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1348 0 0 146 1494
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007865
X-RAY DIFFRACTIONc_angle_deg1.32016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.530.37300.389263293
2.53-2.560.389410.423293334
2.56-2.60.379370.393302339
2.6-2.630.458290.454358387
2.63-2.670.472620.398333395
2.67-2.710.389440.392376420
2.71-2.750.348490.378452501
2.75-2.80.518360.329448484
2.8-2.840.356420.333481523
2.84-2.90.306400.29525565
2.9-2.950.371470.278490537
2.95-3.010.369470.332496543
3.01-3.080.463630.313512575
3.08-3.150.449440.289525569
3.15-3.230.342450.319528573
3.23-3.310.388490.281530579
3.31-3.410.372520.296550602
3.41-3.520.298690.278538607
3.52-3.640.284500.215512562
3.64-3.790.247720.188548620
3.79-3.960.283530.236536589
3.96-4.170.222440.187557601
4.17-4.430.225630.169550613
4.43-4.760.254500.181559609
4.76-5.240.23510.169555606
5.24-5.980.355620.286551613
5.98-7.460.273680.282551619
7.46-200.259670.212544611
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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