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- PDB-4hj5: Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ss... -

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Basic information

Entry
Database: PDB / ID: 4hj5
TitleCrystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTTCGGT)
Components
  • DNA (5'-D(*GP*GP*TP*TP*TP*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: 2.04 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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*TP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)19,9602
Polymers19,9602
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-12 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.873, 59.244, 65.763
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*TP*CP*GP*GP*T)-3')


Mass: 2777.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: variation of S. pombe telomeric sequence / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35% PEG 6000, 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: Feb 7, 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: 2.04→50 Å / Num. all: 10598 / Num. obs: 9855 / % possible obs: 93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.077 / Χ2: 1.88 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.122.50.4119780.808195
2.12-2.212.40.3579820.879195.9
2.21-2.312.40.2619870.985195.6
2.31-2.432.50.2149981.176194.7
2.43-2.582.50.169771.307194
2.58-2.782.50.1389981.829195
2.78-3.062.50.0999752.181192.8
3.06-3.512.40.0759613.202190.2
3.51-4.422.30.0569653.472188.6
4.42-502.20.04510343.441189.1

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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: 4HIK

4hik


Resolution: 2.04→29.951 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.31 / σ(F): 0 / Phase error: 25.83 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 951 10 %random
Rwork0.226 ---
all0.2295 9833 --
obs0.2295 9514 89.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.944 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 75.55 Å2 / Biso mean: 38.5819 Å2 / Biso min: 18.28 Å2
Baniso -1Baniso -2Baniso -3
1-5.9957 Å2-0 Å2-0 Å2
2---1.4473 Å20 Å2
3----5.2647 Å2
Refinement stepCycle: LAST / Resolution: 2.04→29.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 184 0 93 1441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081406
X-RAY DIFFRACTIONf_angle_d1.0971941
X-RAY DIFFRACTIONf_chiral_restr0.076202
X-RAY DIFFRACTIONf_plane_restr0.004215
X-RAY DIFFRACTIONf_dihedral_angle_d16.845531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0397-2.14720.35061210.30771082120381
2.1472-2.28170.29671340.28211207134190
2.2817-2.45780.32411360.24921217135391
2.4578-2.7050.30311360.25841251138793
2.705-3.09610.29991400.2431264140492
3.0961-3.89940.25621390.20241245138490
3.8994-29.95450.21091450.20181297144289

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