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- PDB-7c4r: Crystal structure of hydrogen peroxide treated zebrafish TRF2 com... -

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Basic information

Entry
Database: PDB / ID: 7c4r
TitleCrystal structure of hydrogen peroxide treated zebrafish TRF2 complexed with DNA
Components
  • DNA (5'-D(*D*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*AP*DP*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*A)-3')
  • DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*G)-3')
  • DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*G)-3')
  • Terfa protein
KeywordsDNA BINDING PROTEIN / zebrafish TRF2 / Telomere DNA / complex / hydrogen peroxide treatment.
Function / homology
Function and homology information


negative regulation of telomere maintenance via recombination / telomeric loop formation / cell cycle / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / regulation of telomere maintenance via telomerase / double-stranded telomeric DNA binding ...negative regulation of telomere maintenance via recombination / telomeric loop formation / cell cycle / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / regulation of telomere maintenance via telomerase / double-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / protein localization to chromosome, telomeric region / protein homodimerization activity
Similarity search - Function
Telomeric repeat-binding factor 2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-like domain profile. / Myb-type HTH DNA-binding domain profile. / Myb domain / 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
DNA / DNA (> 10) / Terfa protein
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsJin, Z. / Park, J.H. / Yun, J.H. / Park, S.Y. / Lee, W.
CitationJournal: To Be Published
Title: Crystal structure of hydrogen peroxide treated zebrafish TRF2 myb-domain complexed with DNA
Authors: Jin, Z. / Park, J.H. / Yun, J.H. / Park, S.Y. / Lee, W.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
A: Terfa protein
C: DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*G)-3')
D: DNA (5'-D(*D*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*AP*DP*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*A)-3')
B: Terfa protein
E: DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*G)-3')
F: DNA (5'-D(*D*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*AP*DP*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,0356
Polymers27,0356
Non-polymers00
Water1086
1
A: Terfa protein
C: DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*G)-3')
D: DNA (5'-D(*D*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*AP*DP*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,8463
Polymers13,8463
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-19 kcal/mol
Surface area6710 Å2
MethodPISA
2
B: Terfa protein
E: DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*G)-3')
F: DNA (5'-D(*D*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*AP*DP*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,1883
Polymers13,1883
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-15 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.901, 63.901, 140.234
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Terfa protein / Zebrafish TELOMERIC REPEAT BINDING FACTOR 2


Mass: 6521.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: terfa / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QRH9
#2: DNA chain DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*G)-3')


Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*D*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*AP*DP*CP*DP*CP*DP*CP*DP*TP*DP*AP*DP*A)-3')


Mass: 3551.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*D*TP*DP*TP*DP*AP*DP*GP*DP*GP*DP*GP*DP*TP*DP*TP*DP*AP*DP*G)-3')


Mass: 3115.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20-25% (w/v) polyethylene glycol 3000, 100 mM Sodium acetate/acetic acid

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→46.753 Å / Num. obs: 12129 / % possible obs: 93.88 % / Redundancy: 3.6 % / Biso Wilson estimate: 55.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.65
Reflection shellResolution: 2.44→2.537 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 1167 / % possible all: 83

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W0U

1w0u


Resolution: 2.44→46.745 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 30.51
RfactorNum. reflection% reflection
Rfree0.2571 1205 9.93 %
Rwork0.2272 --
obs0.2302 12129 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.13 Å2 / Biso mean: 55.0391 Å2 / Biso min: 32.66 Å2
Refinement stepCycle: final / Resolution: 2.44→46.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 931 0 6 1853
Biso mean---50.29 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031981
X-RAY DIFFRACTIONf_angle_d0.4892858
X-RAY DIFFRACTIONf_chiral_restr0.029307
X-RAY DIFFRACTIONf_plane_restr0.002198
X-RAY DIFFRACTIONf_dihedral_angle_d22.025997
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.44-2.53770.4121150.3474105283
2.5377-2.65320.31841270.3208114590
2.6532-2.7930.32311320.3134115191
2.793-2.9680.34151370.3046118494
2.968-3.19710.35031320.2773122796
3.1971-3.51870.2671360.2267123797
3.5187-4.02770.28391370.2214126497
4.0277-5.07340.20831380.1951128598
5.0734-46.7450.19351510.1856137998

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