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- PDB-4zmi: Crystal structure of the Helical domain of S. pombe Taz1 -

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Basic information

Entry
Database: PDB / ID: 4zmi
TitleCrystal structure of the Helical domain of S. pombe Taz1
ComponentsTelomere length regulator taz1
KeywordsDNA BINDING PROTEIN / telomere / helical-domain
Function / homology
Function and homology information


meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / mitotic telomere maintenance via semi-conservative replication / shelterin complex / double-stranded telomeric DNA binding ...meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / mitotic telomere tethering at nuclear periphery / meiotic attachment of telomere to nuclear envelope / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / mitotic telomere maintenance via semi-conservative replication / shelterin complex / double-stranded telomeric DNA binding / telomere capping / telomeric DNA binding / telomere maintenance / nuclear periphery / molecular adaptor activity / chromatin / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
: / Telomere length regulator taz1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsDeng, W. / Wu, J. / Wang, F. / Lei, M.
CitationJournal: Cell Res. / Year: 2015
Title: Fission yeast telomere-binding protein Taz1 is a functional but not a structural counterpart of human TRF1 and TRF2.
Authors: Deng, W. / Wu, J. / Wang, F. / Kanoh, J. / Dehe, P.M. / Inoue, H. / Chen, J. / Lei, M.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Assembly

Deposited unit
A: Telomere length regulator taz1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0263
Polymers26,9431
Non-polymers832
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.010, 160.102, 50.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Telomere length regulator taz1


Mass: 26942.648 Da / Num. of mol.: 1 / Fragment: Helical domain (UNP RESIDUES 127-361)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: taz1, myb, myb1, SPAC16A10.07c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P79005
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.4
Details: 100 mM Tris-HCl pH7.0, 18% PEG 3350, 300mM KNO3, 10 mM Co(NH4)6Cl3, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0000, 0.97898, 0.97953, 0.98341
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978981
30.979531
40.983411
ReflectionResolution: 2.25→100 Å / Num. obs: 13012 / % possible obs: 96.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 59.22 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.518 / Net I/av σ(I): 57.905 / Net I/σ(I): 19.7 / Num. measured all: 87731
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.25-2.35.40.3737070.96480.3
2.3-2.365.90.2617951.01590.1
2.36-2.426.30.238531.02896.6
2.42-2.56.80.1838671.06399.1
2.5-2.5870.1428821.06999.9
2.58-2.677.10.118861.134100
2.67-2.777.20.0868901.134100
2.77-2.97.20.0698871.179100
2.9-3.057.10.0538831.275100
3.05-3.257.10.0459121.363100
3.25-3.57.10.0398891.527100
3.5-3.8570.0398991.916100
3.85-4.46.80.0459053.0299.9
4.4-5.556.70.0399292.65799.8
5.55-10060.0338282.16584.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.3→39.107 Å / FOM work R set: 0.7754 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 611 4.97 %
Rwork0.1936 11678 -
obs0.1956 12289 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.02 Å2 / Biso mean: 79.43 Å2 / Biso min: 34.32 Å2
Refinement stepCycle: final / Resolution: 2.3→39.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 2 43 1942
Biso mean--46.43 81.39 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081940
X-RAY DIFFRACTIONf_angle_d1.1662628
X-RAY DIFFRACTIONf_chiral_restr0.077300
X-RAY DIFFRACTIONf_plane_restr0.004334
X-RAY DIFFRACTIONf_dihedral_angle_d15.497708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.53160.32271540.23782798295296
2.5316-2.89780.28441440.225729523096100
2.8978-3.65050.24291570.216629633120100
3.6505-39.11260.20961560.17342965312195
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)
12.3417-0.9627-0.03134.1055-0.45742.8372-0.15950.0220.05380.4819-0.0664-0.65540.08920.22220.00280.38970.1118-0.08960.45150.09750.4852-18.4695-21.037411.3927
20.0865-0.18350.14990.1064-0.09470.03570.05790.1483-0.24270.0367-0.02530.04150.22210.0666-0.00020.57620.13970.01980.49550.07630.4995-21.7096-23.71668.3963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 127:361)A127 - 361
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 501:543)A501 - 543

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