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- PDB-8ipp: Crystal structure of the complex between an ankyrin and a paralle... -

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Basic information

Entry
Database: PDB / ID: 8ipp
TitleCrystal structure of the complex between an ankyrin and a parallel G-quadruplex
Components
  • 93del-T12
  • DARPin protein 2E4
KeywordsDNA BINDING PROTEIN/DNA / G-quadruplex / DARPins / parallel / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsNgo, K.H. / Liew, C.W. / Heddi, B. / Phan, A.T.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2017-09 Singapore
Ministry of Education (MoE, Singapore)MOE2018-T2-2-029 Singapore
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein.
Authors: Ngo, K.H. / Liew, C.W. / Heddi, B. / Phan, A.T.
History
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 93del-T12
B: DARPin protein 2E4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1627
Polymers19,9962
Non-polymers1665
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-13 kcal/mol
Surface area8330 Å2
Unit cell
Length a, b, c (Å)76.759, 83.587, 31.858
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-103-

K

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Components

#1: DNA chain 93del-T12


Mass: 5131.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein DARPin protein 2E4


Mass: 14864.692 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium chloride, 0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 5.6, 5% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.007→38.41 Å / Num. obs: 14343 / % possible obs: 99.11 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 17.34
Reflection shellResolution: 2.01→2.082 Å / Num. unique obs: 1383 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.007→38.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 10.58 / SU ML: 0.229 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.147
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2238 661 4.62 %
Rwork0.2109 13645 -
all0.212 --
obs-14306 98.25 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.066 Å2
Baniso -1Baniso -2Baniso -3
1--5.306 Å20 Å2-0 Å2
2--12.252 Å2-0 Å2
3----6.947 Å2
Refinement stepCycle: LAST / Resolution: 2.007→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 342 5 86 1395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121375
X-RAY DIFFRACTIONr_angle_refined_deg1.9711.6711937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38823.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13615173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.314155
X-RAY DIFFRACTIONr_chiral_restr0.1390.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02938
X-RAY DIFFRACTIONr_nbd_refined0.3680.2722
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.278
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6270.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.210
X-RAY DIFFRACTIONr_mcbond_it4.1614.669510
X-RAY DIFFRACTIONr_mcangle_it5.3236.959638
X-RAY DIFFRACTIONr_scbond_it5.1614.784863
X-RAY DIFFRACTIONr_scangle_it6.8717.0461298
X-RAY DIFFRACTIONr_lrange_it8.00160.1812412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.007-2.0590.438380.446951X-RAY DIFFRACTION97.0559
2.059-2.1150.363590.38977X-RAY DIFFRACTION99.6154
2.115-2.1760.398390.374921X-RAY DIFFRACTION99.8959
2.176-2.2430.271340.339932X-RAY DIFFRACTION99.8966
2.243-2.3170.296420.341888X-RAY DIFFRACTION99.7854
2.317-2.3980.274480.339844X-RAY DIFFRACTION100
2.398-2.4880.326350.339841X-RAY DIFFRACTION100
2.488-2.590.285310.268792X-RAY DIFFRACTION100
2.59-2.7050.17370.219795X-RAY DIFFRACTION100
2.705-2.8360.227410.209723X-RAY DIFFRACTION100
2.836-2.9890.323440.201693X-RAY DIFFRACTION100
2.989-3.170.246370.173672X-RAY DIFFRACTION100
3.17-3.3880.198350.157616X-RAY DIFFRACTION100
3.388-3.6590.223190.153606X-RAY DIFFRACTION100
3.659-4.0060.19250.146560X-RAY DIFFRACTION100
4.006-4.4760.192240.116498X-RAY DIFFRACTION100
4.476-5.1630.15300.13445X-RAY DIFFRACTION100
5.163-6.310.139180.16387X-RAY DIFFRACTION100
6.31-8.8690.12170.128306X-RAY DIFFRACTION100

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