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

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Basic information

Entry
Database: PDB / ID: 4hik
TitleCrystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTACGGT)
Components
  • DNA (5'-D(*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 / 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 / SYNCHROTRON / MAD / Resolution: 1.636 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

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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*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)20,1572
Polymers20,1572
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-7 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.870, 57.390, 66.170
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: 17369.996 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*GP*T)-3')


Mass: 2786.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric single-stranded DNA / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% w/V PEG 4000, 0.2M ammonium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9799, 0.9801, 0.9428
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.98011
30.94281
ReflectionRedundancy: 4.5 % / Av σ(I) over netI: 50.2 / Number: 179702 / Rmerge(I) obs: 0.041 / Χ2: 2.05 / D res high: 1.64 Å / D res low: 50 Å / Num. obs: 40149 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.455098.510.0241.4724.6
3.534.4599.210.0322.5674.5
3.093.5399.810.043.0664.6
2.83.0910010.0412.8874.6
2.62.810010.0432.5474.6
2.452.610010.0412.1314.7
2.332.4599.910.0432.0814.7
2.232.3399.810.0472.2324.6
2.142.2399.810.052.1224.7
2.072.1499.710.0532.0954.6
22.0799.910.0562.1384.6
1.94299.810.061.9744.6
1.891.9499.810.0752.0574.6
1.851.8999.710.0781.8934.6
1.811.8599.710.0861.6124.7
1.771.8199.610.0961.5224.5
1.731.7799.310.1051.5774.2
1.71.7396.510.1181.6034
1.671.797.410.1251.5583.8
1.641.6793.810.1341.4033.6
ReflectionResolution: 1.636→50 Å / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Χ2: 2.05 / Net I/σ(I): 26.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.64-1.673.60.13419161.403193.8
1.67-1.73.80.12519431.558197.4
1.7-1.7340.11819651.603196.5
1.73-1.774.20.10519831.577199.3
1.77-1.814.50.09620231.522199.6
1.81-1.854.70.08620221.612199.7
1.85-1.894.60.07820471.893199.7
1.89-1.944.60.07519932.057199.8
1.94-24.60.0620311.974199.8
2-2.074.60.05620172.138199.9
2.07-2.144.60.05320322.095199.7
2.14-2.234.70.0520162.122199.8
2.23-2.334.60.04720232.232199.8
2.33-2.454.70.04320182.081199.9
2.45-2.64.70.04120262.1311100
2.6-2.84.60.04320292.5471100
2.8-3.094.60.04120152.8871100
3.09-3.534.60.0420193.066199.8
3.53-4.454.50.03220232.567199.2
4.45-504.60.02420081.472198.5

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.74 Å / D res low: 5.74 Å / FOM : 0.704 / Reflection: 17982
Phasing MAD set

Highest resolution: 5.74 Å / Lowest resolution: 1.74 Å

IDR cullis centricR kraut acentricFOM FOM acentricFOM centricPower (kW)
PK_iso0.6410.0350.2630.2470.3761.13
IP_iso0.530.0230.3770.3590.5121.76

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.636→35.348 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.19 / σ(F): 0.05 / Phase error: 19.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1051 5 %random
Rwork0.1935 ---
all0.1947 21007 --
obs0.1947 21007 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.904 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 70.03 Å2 / Biso mean: 18.4056 Å2 / Biso min: 4.69 Å2
Baniso -1Baniso -2Baniso -3
1-4.0568 Å2-0 Å2-0 Å2
2---3.0854 Å20 Å2
3----2.9514 Å2
Refinement stepCycle: LAST / Resolution: 1.636→35.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 185 0 175 1529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061413
X-RAY DIFFRACTIONf_angle_d1.0581949
X-RAY DIFFRACTIONf_chiral_restr0.075202
X-RAY DIFFRACTIONf_plane_restr0.004215
X-RAY DIFFRACTIONf_dihedral_angle_d15.952536
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 (%)
1.6357-1.71010.2891110.23762121223284
1.7101-1.80030.25741290.2072439256895
1.8003-1.91310.22131310.18522482261398
1.9131-2.06080.1841310.17522503263498
2.0608-2.26810.21471340.18752533266799
2.2681-2.59630.22381350.198625852720100
2.5963-3.27060.22611370.207125912728100
3.2706-35.35670.19791430.18472702284599

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