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- PDB-2qhb: Crystal structure of NgTRF complexed with telomeric DNA -

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Basic information

Entry
Database: PDB / ID: 2qhb
TitleCrystal structure of NgTRF complexed with telomeric DNA
Components
  • 5'-D(P*CP*CP*CP*TP*AP*AP*A)-3'
  • 5'-D(P*TP*TP*TP*AP*GP*GP*G)-3'
  • Telomere binding protein TBP1
KeywordsDNA BINDING PROTEIN/DNA / plant / PROTEIN-DNA COMPLEX / DOUBLE HELIX / telomere binding protein / NgTRF / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


green leaf volatile biosynthetic process / telomeric DNA binding / transcription cis-regulatory region binding / regulation of DNA-templated transcription
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
DNA / Telomere binding protein TBP1
Similarity search - Component
Biological speciesNicotiana glutinosa (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCho, H.-S. / Byun, J.-S. / Jun, S.-H.
CitationJournal: To be Published
Title: Complex structure of plant telomere bindig protein, NgTRF and telomere DNA
Authors: Cho, H.-S. / Byun, J.-S. / Jun, S.-H. / Han, W. / Lee, W.
History
DepositionJul 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.3Feb 17, 2021Group: Derived calculations / Source and taxonomy
Category: entity_src_gen / ndb_struct_na_base_pair_step / pdbx_entity_src_syn
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _ndb_struct_na_base_pair_step.roll
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: 5'-D(P*TP*TP*TP*AP*GP*GP*G)-3'
D: 5'-D(P*CP*CP*CP*TP*AP*AP*A)-3'
E: 5'-D(P*TP*TP*TP*AP*GP*GP*G)-3'
F: 5'-D(P*CP*CP*CP*TP*AP*AP*A)-3'
A: Telomere binding protein TBP1
B: Telomere binding protein TBP1


Theoretical massNumber of molelcules
Total (without water)28,5736
Polymers28,5736
Non-polymers00
Water1,874104
1
C: 5'-D(P*TP*TP*TP*AP*GP*GP*G)-3'
D: 5'-D(P*CP*CP*CP*TP*AP*AP*A)-3'
B: Telomere binding protein TBP1


Theoretical massNumber of molelcules
Total (without water)14,2863
Polymers14,2863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-15 kcal/mol
Surface area7570 Å2
MethodPISA
2
E: 5'-D(P*TP*TP*TP*AP*GP*GP*G)-3'
F: 5'-D(P*CP*CP*CP*TP*AP*AP*A)-3'
A: Telomere binding protein TBP1


Theoretical massNumber of molelcules
Total (without water)14,2863
Polymers14,2863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.844, 70.844, 68.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: DNA chain 5'-D(P*TP*TP*TP*AP*GP*GP*G)-3'


Mass: 2168.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(P*CP*CP*CP*TP*AP*AP*A)-3'


Mass: 2066.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Telomere binding protein TBP1


Mass: 10051.410 Da / Num. of mol.: 2 / Fragment: residues 574-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana glutinosa (plant) / Gene: NgTRF / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q84ZU4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 6.5
Details: 50mM CaCl2, 28% PEG MME 550, 0.1M Bis-tris pH6.5, EVAPORATION, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1CaCl211
2PEG MME 55011
3Bis-trisBis-tris methane11
4H2O11
5CaCl212
6PEG MME 55012
7Bis-trisBis-tris methane12
8H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2006
RadiationMonochromator: si 4-crystal channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15094 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Rsym value: 0.095
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2 % / Num. unique all: 1293 / Rsym value: 0.23

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CKX

2ckx


Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflectionSelection details
Rfree0.264 754 RANDOM
Rwork0.251 --
obs-15094 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 578 0 104 2091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_bond_d0.007

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