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- PDB-4hj9: Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ss... -

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Basic information

Entry
Database: PDB / ID: 4hj9
TitleCrystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (CGGTTACGGT)
Components
  • DNA (5'-D(*CP*GP*GP*TP*TP*AP*CP*GP*GP*T)-3')
  • Protection of telomeres protein 1
KeywordsDNA BINDING PROTEIN / specificity / plasticity / promiscuity / OB-fold / ssDNA-binding / single-stranded telomeric DNA
Function / homology
Function and homology information


Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / shelterin complex / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping ...Removal of the Flap Intermediate from the C-strand / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / shelterin complex / regulation of telomere maintenance via telomerase / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / telomere maintenance / nucleus / cytosol
Similarity search - Function
Protection of telomeres protein 1, ssDNA-binding domain / ssDNA-binding domain of telomere protection protein / Protection of telomeres protein 1 / Telomeric single stranded DNA binding POT1/Cdc13 / Telomeric single stranded DNA binding POT1/CDC13 / Telomeric single stranded DNA binding POT1/CDC13 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / Protection of telomeres protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDickey, T.H. / Wuttke, D.S.
CitationJournal: Structure / Year: 2013
Title: Nonspecific Recognition Is Achieved in Pot1pC through the Use of Multiple Binding Modes.
Authors: Dickey, T.H. / McKercher, M.A. / Wuttke, D.S.
History
DepositionOct 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protection of telomeres protein 1
B: DNA (5'-D(*CP*GP*GP*TP*TP*AP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,2582
Polymers20,2582
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-6 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.996, 57.469, 66.152
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 Protection of telomeres protein 1


Mass: 17182.414 Da / Num. of mol.: 1
Fragment: Pot1pC, partial DNA binding domain, residues 198-339
Mutation: V199D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972h- / Gene: pot1, SPAC26H5.06 / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O13988
#2: DNA chain DNA (5'-D(*CP*GP*GP*TP*TP*AP*CP*GP*GP*T)-3')


Mass: 3076.014 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric single-stranded DNA, +1 5' variant / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 6000, 0.2M ammonium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 21, 2011
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 17399 / Num. obs: 17235 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.047 / Χ2: 1.431 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.77-1.832.90.51216240.647195.5
1.83-1.913.20.35117150.785199.9
1.91-1.993.20.2416951.014199.9
1.99-2.13.20.1617191.189199.8
2.1-2.233.20.12217061.357199.8
2.23-2.43.30.09217151.631199.9
2.4-2.643.30.07117361.775199.9
2.64-3.033.30.0517401.766199.3
3.03-3.813.30.03617421.86198.4
3.81-503.10.03318432.049198.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HIK

4hik


Resolution: 1.85→31.232 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.2 / σ(F): 0 / Phase error: 22.16 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 1484 10.01 %random
Rwork0.2006 ---
all0.2045 15128 --
obs0.2045 14821 97.47 %-
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.734 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 87.48 Å2 / Biso mean: 36.0771 Å2 / Biso min: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1-8.4058 Å2-0 Å2-0 Å2
2---2.5709 Å20 Å2
3----5.8349 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 204 0 123 1501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071448
X-RAY DIFFRACTIONf_angle_d1.1252001
X-RAY DIFFRACTIONf_chiral_restr0.081208
X-RAY DIFFRACTIONf_plane_restr0.004219
X-RAY DIFFRACTIONf_dihedral_angle_d18.296554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.90970.30951290.21991151128093
1.9097-1.9780.26991300.19771152128294
1.978-2.05720.26931310.18861179131096
2.0572-2.15080.26341320.21197132998
2.1508-2.26410.26461310.20291183131498
2.2641-2.40590.23951370.20191217135499
2.4059-2.59160.21651360.19861233136999
2.5916-2.85230.28261350.20121220135599
2.8523-3.26460.23891380.21081235137399
3.2646-4.11160.21351390.18561259139898
4.1116-31.23590.23211460.20821311145799

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