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- PDB-3k0x: Crystal structure of telomere capping protein Ten1 from Saccharom... -

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Basic information

Entry
Database: PDB / ID: 3k0x
TitleCrystal structure of telomere capping protein Ten1 from Saccharomyces pombe
ComponentsProtein Ten1
KeywordsPROTEIN BINDING / beta barrel / ob fold / telomere capping / Chromosomal protein / Nucleus / Telomere
Function / homology
Function and homology information


CST complex / telomere cap complex / chromosome, telomeric repeat region / single-stranded telomeric DNA binding / telomere capping
Similarity search - Function
CST complex subunit Ten1, fungal / Telomere capping, CST complex subunit / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Protein ten1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.7 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Ten1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5659
Polymers11,5491
Non-polymers1,0158
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)64.304, 64.304, 66.242
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-201-

IOD

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Components

#1: Protein Protein Ten1


Mass: 11549.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC1393.14, ten1 / Plasmid: pET duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C5Y7
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: 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: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2 M Potassium nitrate, 25% PEG 3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 8, 2009
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.7→22.08 Å / Num. obs: 10634 / % possible obs: 94.5 % / Redundancy: 4.5 % / Rsym value: 0.048 / Net I/σ(I): 10.205
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.792.70.3362.2306111470.33669.5
1.79-1.93.90.2592.8563114350.25993.1
1.9-2.034.80.1534.7702314710.153100
2.03-2.194.80.0997.3660113670.099100
2.19-2.44.90.0769.1608112490.076100
2.4-2.694.90.0589.8554211200.058100
2.69-3.150.04115.249859990.041100
3.1-3.85.10.03415.442308350.034100
3.8-5.385.10.02717.533696630.027100
5.38-22.0850.02717.117553480.02798.8

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.59 Å / D res low: 25.67 Å / FOM : 0.568 / FOM acentric: 0.558 / FOM centric: 0 / Reflection: 11363 / Reflection acentric: 10395 / Reflection centric: 0
Phasing dmFOM : 0.74 / FOM acentric: 0.74 / FOM centric: 0 / Reflection: 11366 / Reflection acentric: 11366 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
4.5-25.6690.930.93584584
2.8-4.50.910.9118281828
2.3-2.80.780.7822872287
2-2.30.670.6723392339
1.7-20.610.6135403540
1.6-1.70.860.86788788

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.12data scaling
PHASERphasing
RESOLVE2.13phasing
CNSrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
RefinementMethod to determine structure: SAD / Resolution: 1.7→20 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.238 1056 9.4 %
Rwork0.188 --
all-10634 -
obs-10630 94.6 %
Solvent computationBsol: 66.185 Å2
Displacement parametersBiso max: 77.25 Å2 / Biso mean: 24.188 Å2 / Biso min: 2.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.465 Å2-0 Å20 Å2
2--0.465 Å20 Å2
3----0.93 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 8 146 928
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.016
LS refinement shellResolution: 1.7→1.73 Å
RfactorNum. reflection
Rfree0.4876 26
Rwork0.4558 -
obs-286
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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