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- PDB-5dof: Crystal structure of Tetrahymena p19 -

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Basic information

Entry
Database: PDB / ID: 5dof
TitleCrystal structure of Tetrahymena p19
ComponentsTelomerase-associated protein 19
KeywordsDNA BINDING PROTEIN / telomerase / OB fold / Tetrahymena
Function / homologytelomerase holoenzyme complex / telomere maintenance via telomerase / chromosome, telomeric region / Telomerase-associated protein of 19 kDa
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsWan, B. / Tang, T. / Wu, J. / Lei, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The Tetrahymena telomerase p75-p45-p19 subcomplex is a unique CST complex.
Authors: Wan, B. / Tang, T. / Upton, H. / Shuai, J. / Zhou, Y. / Li, S. / Chen, J. / Brunzelle, J.S. / Zeng, Z. / Collins, K. / Wu, J. / Lei, M.
History
DepositionSep 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomerase-associated protein 19
B: Telomerase-associated protein 19
C: Telomerase-associated protein 19
D: Telomerase-associated protein 19


Theoretical massNumber of molelcules
Total (without water)77,6554
Polymers77,6554
Non-polymers00
Water11,061614
1
A: Telomerase-associated protein 19


Theoretical massNumber of molelcules
Total (without water)19,4141
Polymers19,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomerase-associated protein 19


Theoretical massNumber of molelcules
Total (without water)19,4141
Polymers19,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Telomerase-associated protein 19


Theoretical massNumber of molelcules
Total (without water)19,4141
Polymers19,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Telomerase-associated protein 19


Theoretical massNumber of molelcules
Total (without water)19,4141
Polymers19,4141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-34 kcal/mol
Surface area29990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.732, 128.631, 75.328
Angle α, β, γ (deg.)90.000, 105.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Telomerase-associated protein 19 / p19


Mass: 19413.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP19 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D2CVN7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7 / Details: 4.0 M sodium formate pH 7.0, 2% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 83371 / % possible obs: 99.1 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.029 / Rrim(I) all: 0.081 / Χ2: 1.011 / Net I/av σ(I): 27.28 / Net I/σ(I): 8.9 / Num. measured all: 619166
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.69-1.726.70.65735010.8350.270.7120.86382.8
1.72-1.757.40.61341480.8910.2420.6590.856100
1.75-1.787.40.53142300.910.2090.5720.881100
1.78-1.827.40.43241510.9420.170.4650.896100
1.82-1.867.40.35942570.9510.1410.3860.902100
1.86-1.97.40.29741110.9680.1170.3190.927100
1.9-1.957.50.23742500.9780.0930.2540.957100
1.95-27.50.1941680.9850.0750.2040.968100
2-2.067.50.15941940.9870.0620.1710.98100
2.06-2.137.50.13641920.990.0530.1460.984100
2.13-2.217.50.11441660.9930.0450.1230.984100
2.21-2.297.50.09842530.9940.0380.1050.973100
2.29-2.47.50.08942090.9950.0350.0950.958100
2.4-2.527.50.0841790.9950.0310.0860.94100
2.52-2.687.50.07142040.9960.0280.0770.97100
2.68-2.897.50.06842170.9960.0260.0731.097100
2.89-3.187.50.0742230.9960.0270.0751.477100
3.18-3.647.40.06442120.9960.0250.0681.55100
3.64-4.597.40.04742230.9980.0180.051.075100
4.59-507.30.04342830.9980.0170.0460.929100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.244 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 4060 5 %RANDOM
Rwork0.1768 ---
obs0.1789 77441 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.38 Å2 / Biso mean: 17.545 Å2 / Biso min: 3.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.11 Å2
2---0.27 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.7→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5121 0 0 614 5735
Biso mean---28.86 -
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195221
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.9417023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2955605
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5625.729295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60615971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1691514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023956
X-RAY DIFFRACTIONr_rigid_bond_restr1.82935221
X-RAY DIFFRACTIONr_sphericity_free19.635199
X-RAY DIFFRACTIONr_sphericity_bonded9.63255536
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 269 -
Rwork0.229 5258 -
all-5527 -
obs--92.22 %

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