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- PDB-7c4p: Crystal structure of DBD plasma treated zebrafish TRF2 myb-domain... -

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Basic information

Entry
Database: PDB / ID: 7c4p
TitleCrystal structure of DBD plasma treated zebrafish TRF2 myb-domain complexed with DNA
Components
  • DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
  • DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
  • Telomere repeat factor a
  • Terfa protein
KeywordsDNA BINDING PROTEIN / zebrafish TRF2 / telomeric DNA / complex.
Function / homology
Function and homology information


negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomeric D-loop disassembly / cell cycle / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase ...negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomeric D-loop disassembly / cell cycle / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / G-rich strand telomeric DNA binding / protein localization to chromosome, telomeric region / telomeric DNA binding / 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 / Telomere repeat factor a
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsJin, Z. / Park, J.H. / Yun, J.H. / Park, S.Y. / Lee, W.
CitationJournal: To Be Published
Title: Crystal structure of DBD plasma 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: Telomere repeat factor a
C: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
D: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')
B: Terfa protein
E: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
F: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,2976
Polymers27,2976
Non-polymers00
Water1,06359
1
A: Telomere repeat factor a
C: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
D: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,0103
Polymers14,0103
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-18 kcal/mol
Surface area6820 Å2
MethodPISA
2
B: Terfa protein
E: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
F: DNA (5'-D(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,2873
Polymers13,2873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-14 kcal/mol
Surface area6740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.994, 63.994, 142.418
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Telomere repeat factor a / Zebrafish TELOMERIC REPEAT BINDING FACTOR 2


Mass: 6684.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: terfa / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JGS4
#4: Protein Terfa protein / Zebrafish TELOMERIC REPEAT BINDING FACTOR 2


Mass: 6620.800 Da / Num. of mol.: 1
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

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DNA chain , 3 types, 4 molecules CDFE

#2: DNA chain DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*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(*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*A)-3')


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


Mass: 3115.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 59 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
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: 1.9946→43.736 Å / Num. obs: 23161 / % possible obs: 97.56 % / Redundancy: 4.9 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 26.86
Reflection shellResolution: 1.995→2.045 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 1368

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Processing

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

1w0u


Resolution: 1.995→43.736 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.73
RfactorNum. reflection% reflection
Rfree0.2597 1989 8.59 %
Rwork0.2304 --
obs0.233 23161 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.99 Å2 / Biso mean: 42.651 Å2 / Biso min: 26.62 Å2
Refinement stepCycle: final / Resolution: 1.995→43.736 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 928 0 59 1922
Biso mean---40.95 -
Num. residues----156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061998
X-RAY DIFFRACTIONf_angle_d0.822882
X-RAY DIFFRACTIONf_chiral_restr0.044309
X-RAY DIFFRACTIONf_plane_restr0.005201
X-RAY DIFFRACTIONf_dihedral_angle_d23.1821006
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.995-2.04450.3931160.3254125284
2.0445-2.09980.3251420.3027146896
2.0998-2.16160.33361380.2846150799
2.1616-2.23130.29181420.2815152799
2.2313-2.31110.3551410.2778150799
2.3111-2.40360.33371450.2842151099
2.4036-2.5130.38471410.2928152299
2.513-2.64550.32481430.29781526100
2.6455-2.81120.29781430.28121527100
2.8112-3.02820.32161500.2887153899
3.0282-3.33280.31591420.2408151797
3.3328-3.81490.22311440.2228155598
3.8149-4.80540.21521450.1884155298
4.8054-43.7360.18951570.1701166499

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