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- PDB-2ckx: Crystal structure of NgTRF1, double-stranded telomeric repeat bin... -

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Basic information

Entry
Database: PDB / ID: 2ckx
TitleCrystal structure of NgTRF1, double-stranded telomeric repeat binding factor from Nicotiana tabacum.
ComponentsTELOMERE BINDING PROTEIN TBP1
KeywordsNUCLEAR PROTEIN
Function / homology
Function and homology information


green leaf volatile biosynthetic process / telomeric DNA binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Telomere repeat-binding protein, plant / Serum Albumin; Chain A, Domain 1 - #220 / Myb-like domain profile. / Myb-type HTH DNA-binding domain profile. / Serum Albumin; Chain A, Domain 1 / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Ubiquitin domain profile. ...Telomere repeat-binding protein, plant / Serum Albumin; Chain A, Domain 1 - #220 / Myb-like domain profile. / Myb-type HTH DNA-binding domain profile. / Serum Albumin; Chain A, Domain 1 / Myb domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Telomere binding protein / Telomere binding protein TBP1
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsByun, J.-S. / Cho, H.-S.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structure of the DNA-Binding Domain of Ngtrf1 Reveals Unique Features of Plant Telomere-Binding Proteins.
Authors: Ko, S. / Jun, S. / Bae, H. / Byun, J.-S. / Han, W. / Park, H. / Yang, S.W. / Park, S. / Jeon, Y.H. / Cheong, C. / Kim, W.T. / Lee, W. / Cho, H.-S.
History
DepositionApr 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 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

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Assembly

Deposited unit
A: TELOMERE BINDING PROTEIN TBP1


Theoretical massNumber of molelcules
Total (without water)9,5951
Polymers9,5951
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.122, 48.265, 52.006
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TELOMERE BINDING PROTEIN TBP1 / NGTRF1


Mass: 9594.801 Da / Num. of mol.: 1 / Fragment: TELOMERIC DNA BINDING DOMAIN, RESIDUES 578-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Plasmid: PPROEX HT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84ZU4, UniProt: A0ZPR8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.8 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1M TRIS PH 8.5, 25%(W/V) PEG3350

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.8
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 26, 2006 / Details: MIRRORS
RadiationMonochromator: SI FILTER / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 9807 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / % possible all: 96.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 443 4.5 %RANDOM
Rwork0.2101 ---
obs0.2101 8186 83.5 %-
Solvent computationBsol: 28.4199 Å2 / ksol: 0.43026 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.839 Å20 Å20 Å2
2---0.69 Å20 Å2
3----0.149 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 0 99 777
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006924
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.21776
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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