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

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Basic information

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


: / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / regulation of telomere maintenance via telomerase / shelterin complex / single-stranded telomeric DNA binding / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping ...: / telomere cap complex / chromosome, telomeric repeat region / telomerase inhibitor activity / regulation of telomere maintenance via telomerase / shelterin complex / 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: 1.822 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 11, 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 / Item: _software.classification / _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,9292
Polymers19,9292
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-4 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.959, 59.196, 66.093
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*CP*TP*TP*AP*CP*GP*GP*T)-3')


Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric single-stranded DNA, G2C variant / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% w/V PEG 3350, 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: Dec 28, 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: 1.822→50 Å / Num. all: 14900 / Num. obs: 14145 / % possible obs: 95 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Χ2: 1.428 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.83-1.92.50.32112330.72183.8
1.9-1.973.20.25613620.819193.7
1.97-2.063.50.19613930.959194.3
2.06-2.173.50.15313851.002195
2.17-2.313.50.12813881.053195.4
2.31-2.483.50.11214091.173196.2
2.48-2.733.50.09114481.391196.9
2.73-3.133.50.06914491.676197.2
3.13-3.943.40.05414772.44197.7
3.94-503.20.04916012.599198.8

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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 / Resolution: 1.822→30.01 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8491 / SU ML: 0.12 / σ(F): 0 / Phase error: 21.54 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 1373 9.95 %random
Rwork0.2054 ---
all0.207 14900 --
obs0.207 13797 92.31 %-
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.499 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 70.7 Å2 / Biso mean: 26.2916 Å2 / Biso min: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.0054 Å20 Å20 Å2
2--3.9925 Å20 Å2
3----1.9871 Å2
Refinement stepCycle: LAST / Resolution: 1.822→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 182 0 196 1547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071409
X-RAY DIFFRACTIONf_angle_d0.7971942
X-RAY DIFFRACTIONf_chiral_restr0.052202
X-RAY DIFFRACTIONf_plane_restr0.003215
X-RAY DIFFRACTIONf_dihedral_angle_d19.844536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8216-1.88670.39081050.2913951105671
1.8867-1.96220.26971260.2371165129189
1.9622-2.05150.22551370.21121220135792
2.0515-2.15970.24911340.21581221135593
2.1597-2.29490.23451400.21281250139094
2.2949-2.4720.23861400.20771247138794
2.472-2.72070.24731420.21291296143897
2.7207-3.1140.24641440.21281306145097
3.114-3.92190.16911460.18451334148098
3.9219-30.0140.19781590.1951434159399

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