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- PDB-4hj7: Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ss... -

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Basic information

Entry
Database: PDB / ID: 4hj7
TitleCrystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTAGGGT)
Components
  • DNA (5'-D(*GP*GP*TP*TP*AP*GP*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 / 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: 1.783 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*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,0092
Polymers20,0092
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-7 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.756, 58.181, 65.626
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*GP*GP*GP*T)-3')


Mass: 2826.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric single-stranded DNA, C6G variant / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 6000, 0.2M lithium nitrate, 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 8, 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: 1.783→50 Å / Num. all: 15437 / Num. obs: 15354 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.036 / Χ2: 1.031 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.79-1.853.40.19214920.746199.5
1.85-1.933.40.13115140.73199.7
1.93-2.023.40.09715150.907199.7
2.02-2.123.50.07615030.995199.9
2.12-2.263.50.06315301.051199.9
2.26-2.433.50.05415271.1041100
2.43-2.673.50.04515271.0971100
2.67-3.063.50.03515491.15199.8
3.06-3.863.50.02815741.237199.6
3.86-503.40.02416231.247197.1

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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: PDB entry 4HIK

4hik


Resolution: 1.783→17.512 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.19 / σ(F): 0 / Phase error: 17.63 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 1527 10.02 %random
Rwork0.1737 ---
all0.1769 15326 --
obs0.1769 15243 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.296 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 59.53 Å2 / Biso mean: 23.3169 Å2 / Biso min: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.7795 Å2-0 Å2-0 Å2
2--2.029 Å20 Å2
3----1.2495 Å2
Refinement stepCycle: LAST / Resolution: 1.783→17.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 188 0 184 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071417
X-RAY DIFFRACTIONf_angle_d1.1441956
X-RAY DIFFRACTIONf_chiral_restr0.077202
X-RAY DIFFRACTIONf_plane_restr0.005215
X-RAY DIFFRACTIONf_dihedral_angle_d16.98536
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 (%)
1.7828-1.84020.27051290.23141130125992
1.8402-1.90590.23461350.19341218135398
1.9059-1.98210.26621350.17581224135999
1.9821-2.07220.24061370.169812371374100
2.0722-2.18130.19381380.166912491387100
2.1813-2.31770.20111390.171612421381100
2.3177-2.49610.22391390.176812511390100
2.4961-2.74650.21061420.182412741416100
2.7465-3.14190.19641410.170412631404100
3.1419-3.9510.20351410.156412811422100
3.951-17.51290.1821510.17881347149899

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