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- PDB-5xxe: Crystal structure of Poz1 and Tpz1 -

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Basic information

Entry
Database: PDB / ID: 5xxe
TitleCrystal structure of Poz1 and Tpz1
Components
  • Protection of telomeres protein poz1
  • Protection of telomeres protein tpz1
KeywordsDNA BINDING PROTEIN / telomere / sheterin / hub
Function / homology
Function and homology information


telomere-telomerase complex assembly / telomere cap complex / chromosome, telomeric repeat region / shelterin complex / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere maintenance via telomerase / telomere maintenance / telomere organization ...telomere-telomerase complex assembly / telomere cap complex / chromosome, telomeric repeat region / shelterin complex / telomere capping / protein localization to chromosome, telomeric region / telomeric DNA binding / telomere maintenance via telomerase / telomere maintenance / telomere organization / DNA binding / nucleus / cytosol
Similarity search - Function
Adrenocortical dysplasia protein
Similarity search - Domain/homology
Protection of telomeres protein poz1 / Protection of telomeres protein tpz1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsXue, J. / Chen, H. / Wu, J. / Lei, M.
CitationJournal: Cell Res. / Year: 2017
Title: Structure of the fission yeast S. pombe telomeric Tpz1-Poz1-Rap1 complex.
Authors: Xue, J. / Chen, H. / Wu, J. / Takeuchi, M. / Inoue, H. / Liu, Y. / Sun, H. / Chen, Y. / Kanoh, J. / Lei, M.
History
DepositionJul 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protection of telomeres protein poz1
C: Protection of telomeres protein tpz1
B: Protection of telomeres protein poz1
D: Protection of telomeres protein tpz1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,39716
Polymers68,3054
Non-polymers1,09112
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-254 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.641, 97.640, 107.262
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 poz1 / Pot1-associated protein poz1


Mass: 30228.285 Da / Num. of mol.: 2 / Fragment: UNP residues 2-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Strain: 972 / ATCC 24843 / Gene: poz1, SPAC19G12.13c / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O13852
#2: Protein/peptide Protection of telomeres protein tpz1 / Meiotically up-regulated gene 169 protein


Mass: 3924.391 Da / Num. of mol.: 2 / Fragment: UNP residues 477-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tpz1, mug169, SPAC6F6.16c, SPAC6F6.18c / Plasmid: pMAL-C2X / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14246
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 4 Å3/Da / Density % sol: 69.24 % / Mosaicity: 0.358 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5 / Details: 0.1 M Bis-Tris, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 35363 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Χ2: 0.776 / Net I/σ(I): 7 / Num. measured all: 155388
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.594.50.67134890.8520.350.7590.92899.8
2.59-2.694.40.50434590.8910.2650.5710.89899.7
2.69-2.824.20.33834970.9240.1850.3870.87599.7
2.82-2.964.50.24534890.9580.1280.2780.85799.5
2.96-3.154.60.16735030.9780.0860.1880.79299.9
3.15-3.394.50.09335050.9890.0480.1050.78599.8
3.39-3.734.20.05635310.9940.030.0630.73399.6
3.73-4.274.60.03835490.9960.020.0430.71899.6
4.27-5.384.30.02935910.9960.0150.0330.6399.8
5.38-504.20.02337500.9980.0130.0270.55299.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.034 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.256
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 1654 5.1 %RANDOM
Rwork0.2094 ---
obs0.2118 31069 92.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 161.44 Å2 / Biso mean: 49.03 Å2 / Biso min: 13.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.49 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 52 227 4559
Biso mean--93.95 44.63 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194406
X-RAY DIFFRACTIONr_bond_other_d0.0010.024037
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9745901
X-RAY DIFFRACTIONr_angle_other_deg0.89139400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3375501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16524.148229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71715810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.541530
X-RAY DIFFRACTIONr_chiral_restr0.0650.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02926
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 63 -
Rwork0.274 1253 -
all-1316 -
obs--51.45 %

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