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- PDB-5dok: Crystal structure of Tetrahymena p45C -

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Basic information

Entry
Database: PDB / ID: 5dok
TitleCrystal structure of Tetrahymena p45C
ComponentsTelomerase associated protein p45
KeywordsDNA BINDING PROTEIN / telomerase / WH motif / Tetrahymena
Function / homologytelomerase holoenzyme complex / telomere maintenance via telomerase / chromosome, telomeric region / metal ion binding / Telomerase-associated protein of 45 kDa
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 p45
B: Telomerase associated protein p45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0254
Polymers47,9762
Non-polymers492
Water1,18966
1
A: Telomerase associated protein p45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0132
Polymers23,9881
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Telomerase associated protein p45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0132
Polymers23,9881
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Telomerase associated protein p45
B: Telomerase associated protein p45
hetero molecules

A: Telomerase associated protein p45
B: Telomerase associated protein p45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0508
Polymers95,9534
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area11120 Å2
ΔGint-36 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.999, 89.051, 75.888
Angle α, β, γ (deg.)90.000, 108.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21B-516-

HOH

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Components

#1: Protein Telomerase associated protein p45 / p45


Mass: 23988.246 Da / Num. of mol.: 2 / Fragment: WH motif, UNP residues 170-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP45 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6JXI5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.08 M Magnesium acetate tetrahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.5, 15% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20444 / % possible obs: 95.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.19 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.059 / Rrim(I) all: 0.14 / Χ2: 1.493 / Net I/av σ(I): 22.196 / Net I/σ(I): 7.3 / Num. measured all: 107423
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.385.50.73421240.8990.3340.8080.55798.2
2.38-2.485.50.51620650.9250.2350.5680.57898.6
2.48-2.595.40.38520890.9390.1780.4250.6998.5
2.59-2.735.10.28320980.9580.1350.3150.83698
2.73-2.95.10.20620710.9790.0970.2281.07397.9
2.9-3.125.60.16621140.9870.0750.1831.32299.1
3.12-3.445.50.12521410.9890.0580.1381.93699
3.44-3.934.70.10215480.9890.050.1152.59373.3
3.93-4.954.90.07420740.9950.0360.0833.13396.1
4.95-5050.06621200.9960.0310.0742.86596.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→35.953 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1056 5.17 %0
Rwork0.2228 19357 --
obs0.2256 20413 95.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.08 Å2 / Biso mean: 38.8249 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 2.3→35.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 2 66 2884
Biso mean--39.98 41.22 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092864
X-RAY DIFFRACTIONf_angle_d1.2913854
X-RAY DIFFRACTIONf_chiral_restr0.078435
X-RAY DIFFRACTIONf_plane_restr0.006477
X-RAY DIFFRACTIONf_dihedral_angle_d18.7361088
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 (%)
2.3001-2.40480.34181370.24552484262198
2.4048-2.53160.29171110.23862510262198
2.5316-2.69010.28331140.22962507262199
2.6901-2.89770.30121310.2192439257098
2.8977-3.18920.29481560.2372481263799
3.1892-3.65030.28941270.23932356248393
3.6503-4.59750.23851300.20072087221789
4.5975-35.95740.26521500.21382493264397
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1242-0.3529-0.23540.54630.10790.6361-0.0072-0.0589-0.03560.04270.0316-0.081-0.03040.1057-00.2401-0.014-0.01360.2148-0.00010.2611-4.163-4.469575.4018
21.3132-0.039-0.20830.7368-0.18240.8995-0.00150.2663-0.1803-0.0403-0.01320.04530.0030.008500.26960.01260.00340.2846-0.04230.2414-21.2927-10.586151.742
37.2634-1.1989-3.9375.4644-2.95135.945-0.13430.03710.00840.14430.1048-0.0890.0625-0.046600.33020.03450.09640.07730.09020.406-14.1305-7.483564.72
40.1791-0.14380.20530.0842-0.15750.2174-0.04060.18960.0509-0.030.0495-0.00070.00780.11620.00770.20210.02170.04980.19320.04020.1996-14.4024-4.722357.8784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND RESID 177:367A177 - 367
2X-RAY DIFFRACTION2CHAIN B AND RESID 178:366B178 - 366
3X-RAY DIFFRACTION3( CHAIN A AND RESID 401:401 ) OR ( CHAIN B AND RESID 401:401 )A401
4X-RAY DIFFRACTION3( CHAIN A AND RESID 401:401 ) OR ( CHAIN B AND RESID 401:401 )B401
5X-RAY DIFFRACTION4( CHAIN A AND RESID 501:525 ) OR ( CHAIN B AND RESID 501:541 )A501 - 525
6X-RAY DIFFRACTION4( CHAIN A AND RESID 501:525 ) OR ( CHAIN B AND RESID 501:541 )B501 - 541

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