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- PDB-4hj8: Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ss... -

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Basic information

Entry
Database: PDB / ID: 4hj8
TitleCrystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTACGCT)
Components
  • DNA (5'-D(*GP*GP*TP*TP*AP*CP*GP*CP*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 / nuclear telomere cap complex / single-stranded telomeric DNA binding / 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 / nuclear telomere cap complex / single-stranded telomeric DNA binding / 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: 2.043 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(*GP*GP*TP*TP*AP*CP*GP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)19,9292
Polymers19,9292
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-6 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.584, 57.548, 66.575
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(*GP*GP*TP*TP*AP*CP*GP*CP*T)-3')


Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric single-stranded DNA, G8C variant / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% PEG 8000, 0.2M sodium 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: Mar 5, 2012
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.043→50 Å / Num. all: 11338 / Num. obs: 11273 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.073 / Χ2: 1.069 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.123.20.45910930.781198.9
2.12-2.213.30.36911090.827199.8
2.21-2.313.40.30611100.892199.9
2.31-2.433.40.23711140.9131100
2.43-2.583.50.18611130.9971100
2.58-2.783.40.14511211.1371100
2.78-3.063.50.09311251.2641100
3.06-3.513.50.05811361.4051100
3.51-4.423.40.03911601.34199.8
4.42-503.30.02911921.063196.4

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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: 2.043→18.779 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.25 / σ(F): 0 / Phase error: 22.72 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1103 10.07 %random
Rwork0.1923 ---
all0.1962 11245 --
obs0.1962 10956 96.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.137 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 72.23 Å2 / Biso mean: 30.0413 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-8.8786 Å2-0 Å2-0 Å2
2---2.7538 Å2-0 Å2
3----6.1248 Å2
Refinement stepCycle: LAST / Resolution: 2.043→18.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 182 0 125 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071409
X-RAY DIFFRACTIONf_angle_d1.0461942
X-RAY DIFFRACTIONf_chiral_restr0.071202
X-RAY DIFFRACTIONf_plane_restr0.006215
X-RAY DIFFRACTIONf_dihedral_angle_d17.849536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0427-2.13560.3211250.2571093121887
2.1356-2.2480.29831310.23061176130795
2.248-2.38860.27561370.22311220135797
2.3886-2.57260.25271370.21611216135397
2.5726-2.83070.21391380.19711234137298
2.8307-3.23850.25171410.18771275141699
3.2385-4.07330.20541430.169112861429100
4.0733-18.77990.19911510.17841353150499

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