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- PDB-8ipf: Crystal structure of an ankyrin protein that can specifically rec... -

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Basic information

Entry
Database: PDB / ID: 8ipf
TitleCrystal structure of an ankyrin protein that can specifically recognize a parallel G-quadruplex
ComponentsDARPin (2E4)
KeywordsDNA BINDING PROTEIN / G-quadruplex / parallel / DNA
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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: DARPin (2E4)
B: DARPin (2E4)
C: DARPin (2E4)
D: DARPin (2E4)
E: DARPin (2E4)
F: DARPin (2E4)
G: DARPin (2E4)
H: DARPin (2E4)


Theoretical massNumber of molelcules
Total (without water)118,9188
Polymers118,9188
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.300, 59.068, 127.505
Angle α, β, γ (deg.)90.000, 100.565, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
DARPin (2E4)


Mass: 14864.692 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6% v/v ethylene glycol, 0.1 M citric acid pH 3.5, 10% w/v polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.01→49.25 Å / Num. obs: 62810 / % possible obs: 99.12 % / Redundancy: 2 % / Biso Wilson estimate: 28.98 Å2 / CC1/2: 1 / Net I/σ(I): 12.83
Reflection shellResolution: 2.01→2.082 Å / Num. unique obs: 6229 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→49.25 Å / SU ML: 0.1695 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.9907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 3105 4.97 %
Rwork0.2261 59397 -
obs0.2273 62502 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.58 Å2
Refinement stepCycle: LAST / Resolution: 2.01→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7425 0 0 423 7848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127620
X-RAY DIFFRACTIONf_angle_d1.502910312
X-RAY DIFFRACTIONf_chiral_restr0.09711155
X-RAY DIFFRACTIONf_plane_restr0.00731372
X-RAY DIFFRACTIONf_dihedral_angle_d16.93662792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.040.38151450.33732683X-RAY DIFFRACTION99.37
2.04-2.070.41511380.31592683X-RAY DIFFRACTION99.12
2.07-2.110.36541270.31772660X-RAY DIFFRACTION99.29
2.11-2.150.30881130.30222741X-RAY DIFFRACTION99.34
2.15-2.190.28691370.30352699X-RAY DIFFRACTION99.06
2.19-2.230.28941430.28542658X-RAY DIFFRACTION99.15
2.23-2.280.33171360.27752714X-RAY DIFFRACTION99.23
2.28-2.340.28861300.27212639X-RAY DIFFRACTION98.96
2.34-2.390.22421180.25312729X-RAY DIFFRACTION99.06
2.39-2.460.28461420.24562698X-RAY DIFFRACTION98.92
2.46-2.530.26291380.23012657X-RAY DIFFRACTION99.01
2.53-2.610.26671560.21742656X-RAY DIFFRACTION98.94
2.61-2.710.23241680.21922675X-RAY DIFFRACTION98.75
2.71-2.810.25651650.22322726X-RAY DIFFRACTION99.38
2.81-2.940.23691470.22042668X-RAY DIFFRACTION99.22
2.94-3.10.2331370.22942701X-RAY DIFFRACTION99.58
3.1-3.290.24821260.21482729X-RAY DIFFRACTION99.24
3.29-3.550.2471480.20372712X-RAY DIFFRACTION99.27
3.55-3.90.21531370.18972716X-RAY DIFFRACTION99.37
3.9-4.470.1991660.18292715X-RAY DIFFRACTION99.65
4.47-5.620.24461590.2182743X-RAY DIFFRACTION99.66
5.63-49.250.22461290.21162795X-RAY DIFFRACTION97.56

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