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

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Basic information

Entry
Database: PDB / ID: 4hja
TitleCrystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (ACGGTTACGGT)
Components
  • DNA (5'-D(*AP*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 / telomere capping / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding ...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 / telomere capping / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / 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 / DNA (> 10) / Protection of telomeres protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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(*AP*CP*GP*GP*TP*TP*AP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,5722
Polymers20,5722
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-3 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.850, 56.776, 66.258
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(*AP*CP*GP*GP*TP*TP*AP*CP*GP*GP*T)-3')


Mass: 3389.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric single-stranded DNA, +2 5' variant / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 8000, 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: Dec 9, 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: 2→50 Å / Num. all: 12272 / Num. obs: 12182 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Χ2: 1.106 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.10.46311230.75193.4
2.07-2.153.40.36211940.7521100
2.15-2.253.50.29911990.791100
2.25-2.373.50.23712130.8031100
2.37-2.523.50.18512090.871100
2.52-2.713.50.14312130.9851100
2.71-2.993.50.10812221.1531100
2.99-3.423.50.06712211.422199.9
3.42-4.313.50.05112531.7511100
4.31-503.30.04113351.642199.5

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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: 2.1→31.408 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 0 / Phase error: 21.93 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 1043 10.06 %random
Rwork0.1926 ---
all0.1983 10557 --
obs0.1983 10368 98.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.509 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 79.59 Å2 / Biso mean: 27.7296 Å2 / Biso min: 11.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.5949 Å20 Å2-0 Å2
2--1.4791 Å20 Å2
3----2.074 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1177 225 0 138 1540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081462
X-RAY DIFFRACTIONf_angle_d1.2252022
X-RAY DIFFRACTIONf_chiral_restr0.084210
X-RAY DIFFRACTIONf_plane_restr0.004218
X-RAY DIFFRACTIONf_dihedral_angle_d19.622556
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 (%)
2.1-2.21080.29281400.21631241138194
2.2108-2.34920.28721480.20921296144497
2.3492-2.53060.28681420.19761302144498
2.5306-2.78510.30561490.19161324147399
2.7851-3.18770.24921510.1971346149799
3.1877-4.01490.22791530.172413701523100
4.0149-31.4120.21371600.197214461606100

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