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- PDB-3u58: Crystal Structure of the Tetrahymena telomerase processivity fact... -

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Basic information

Entry
Database: PDB / ID: 3u58
TitleCrystal Structure of the Tetrahymena telomerase processivity factor Teb1 AB
Components
  • DNA (5'-D(*GP*GP*GP*T)-3')
  • Tetrahymena Teb1 AB
KeywordsDNA binding protein/dna / tetrahymena / telomerase / Teb1 / processivity factor / DNA binding protein-dna complex
Function / homologyNucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / DNA
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.613 Å
AuthorsZeng, Z. / Huang, J. / Yang, Y. / Lei, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for Tetrahymena telomerase processivity factor Teb1 binding to single-stranded telomeric-repeat DNA.
Authors: Zeng, Z. / Min, B. / Huang, J. / Hong, K. / Yang, Y. / Collins, K. / Lei, M.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetrahymena Teb1 AB
B: Tetrahymena Teb1 AB
C: Tetrahymena Teb1 AB
D: Tetrahymena Teb1 AB
E: DNA (5'-D(*GP*GP*GP*T)-3')
H: DNA (5'-D(*GP*GP*GP*T)-3')
F: DNA (5'-D(*GP*GP*GP*T)-3')
G: DNA (5'-D(*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)104,5918
Polymers104,5918
Non-polymers00
Water1,18966
1
A: Tetrahymena Teb1 AB
E: DNA (5'-D(*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)26,1482
Polymers26,1482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetrahymena Teb1 AB
F: DNA (5'-D(*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)26,1482
Polymers26,1482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tetrahymena Teb1 AB
G: DNA (5'-D(*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)26,1482
Polymers26,1482
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tetrahymena Teb1 AB
H: DNA (5'-D(*GP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)26,1482
Polymers26,1482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.046, 83.110, 82.885
Angle α, β, γ (deg.)108.45, 111.59, 108.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Tetrahymena Teb1 AB


Mass: 24901.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Production host: Escherichia coli (E. coli)
#2: DNA chain
DNA (5'-D(*GP*GP*GP*T)-3')


Mass: 1246.853 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 4.21 Å3/Da / Density % sol: 70.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% PEG6000, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97944 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 162402 / Num. obs: 48660 / % possible obs: 94.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 21.366
Reflection shell
Resolution (Å)Diffraction-ID
2.6-2.691
2.69-2.81
2.8-2.931
2.93-3.081
3.08-3.281
3.28-3.531
3.53-3.881
3.88-4.451
4.45-5.61
5.6-1001

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.613→33.58 Å / SU ML: 0.39 / σ(F): 1.97 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 4901 10.09 %
Rwork0.2191 --
obs0.2232 48595 94.04 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.261 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.613→33.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6980 332 0 66 7378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067493
X-RAY DIFFRACTIONf_angle_d1.13410154
X-RAY DIFFRACTIONf_dihedral_angle_d18.9522793
X-RAY DIFFRACTIONf_chiral_restr0.0861082
X-RAY DIFFRACTIONf_plane_restr0.0031243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6127-2.64240.41151000.3772840X-RAY DIFFRACTION54
2.6424-2.67350.40011370.35061096X-RAY DIFFRACTION70
2.6735-2.70610.36911250.32671138X-RAY DIFFRACTION75
2.7061-2.74030.36761330.34231310X-RAY DIFFRACTION84
2.7403-2.77640.36821710.31551360X-RAY DIFFRACTION87
2.7764-2.81440.37131310.31371419X-RAY DIFFRACTION91
2.8144-2.85460.38851560.30351477X-RAY DIFFRACTION93
2.8546-2.89710.37231690.28821426X-RAY DIFFRACTION96
2.8971-2.94240.31261610.27731516X-RAY DIFFRACTION97
2.9424-2.99060.31421740.27151535X-RAY DIFFRACTION98
2.9906-3.04210.30251530.26911530X-RAY DIFFRACTION98
3.0421-3.09740.33451710.27841530X-RAY DIFFRACTION99
3.0974-3.15690.29771910.251500X-RAY DIFFRACTION99
3.1569-3.22130.32941750.24961537X-RAY DIFFRACTION99
3.2213-3.29130.27151860.23951519X-RAY DIFFRACTION99
3.2913-3.36780.26181630.23711527X-RAY DIFFRACTION98
3.3678-3.4520.27391580.23831603X-RAY DIFFRACTION99
3.452-3.54520.29251720.23361454X-RAY DIFFRACTION99
3.5452-3.64940.26211760.21341542X-RAY DIFFRACTION99
3.6494-3.7670.26751830.20581542X-RAY DIFFRACTION99
3.767-3.90150.2271490.20271536X-RAY DIFFRACTION99
3.9015-4.05740.24191640.19571541X-RAY DIFFRACTION99
4.0574-4.24180.22311740.1811521X-RAY DIFFRACTION99
4.2418-4.46490.22531800.18081524X-RAY DIFFRACTION99
4.4649-4.74390.21631840.16611517X-RAY DIFFRACTION99
4.7439-5.10910.21871710.18061523X-RAY DIFFRACTION99
5.1091-5.6210.21651920.20821541X-RAY DIFFRACTION99
5.621-6.42950.26441620.21511584X-RAY DIFFRACTION99
6.4295-8.08180.24451700.21421511X-RAY DIFFRACTION100
8.0818-33.5830.17511700.17241495X-RAY DIFFRACTION97

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