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- PDB-8tx4: Crystal Structure of rA3G-ssDNA-GA -

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Basic information

Entry
Database: PDB / ID: 8tx4
TitleCrystal Structure of rA3G-ssDNA-GA
Components
  • DNA 22-mer with (5'-D(P*TP*GP*AP*TP*TP)-3')
  • DNA dC->dU-editing enzyme APOBEC-3G
KeywordsHYDROLASE/DNA / DEAMINASE / APOBEC / HYDROLASE / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / : / DNA cytosine deamination / cytidine deaminase activity / transposable element silencing / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus
Similarity search - Function
Novel AID APOBEC clade 2 / : / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / DNA dC->dU-editing enzyme APOBEC-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYang, H. / Pacheco, J.I. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2024
Title: Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain.
Authors: Yang, H. / Pacheco, J. / Kim, K. / Bokani, A. / Ito, F. / Ebrahimi, D. / Chen, X.S.
History
DepositionAug 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3G
B: DNA 22-mer with (5'-D(P*TP*GP*AP*TP*TP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0625
Polymers51,8362
Non-polymers2263
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-90 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.295, 67.977, 127.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA dC->dU-editing enzyme APOBEC-3G / Deoxycytidine deaminase


Mass: 45199.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: APOBEC3G / Production host: Escherichia coli (E. coli)
References: UniProt: M1GSK9, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain DNA 22-mer with (5'-D(P*TP*GP*AP*TP*TP)-3')


Mass: 6636.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-tris propane pH 7.5, 0.2 M Sodium/Potassium phosphate, 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 1.9→63.95 Å / Num. obs: 38683 / % possible obs: 99.68 % / Redundancy: 13.1 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1056 / Rpim(I) all: 0.03001 / Net I/σ(I): 17.48
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.9781 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 3806 / CC1/2: 0.917 / CC star: 0.978 / Rpim(I) all: 0.2812 / % possible all: 99.71

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASERphasing
Cootmodel building
xia2data scaling
xia2data reduction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→63.95 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.3121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218 1888 4.88 %
Rwork0.1747 36777 -
obs0.1767 38665 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.76 Å2
Refinement stepCycle: LAST / Resolution: 1.9→63.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 87 7 333 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583308
X-RAY DIFFRACTIONf_angle_d0.82194508
X-RAY DIFFRACTIONf_chiral_restr0.0529453
X-RAY DIFFRACTIONf_plane_restr0.0071567
X-RAY DIFFRACTIONf_dihedral_angle_d11.0074451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.28031440.26512784X-RAY DIFFRACTION99.8
1.95-2.010.26821490.22822764X-RAY DIFFRACTION99.66
2.01-2.070.24981490.21342784X-RAY DIFFRACTION99.73
2.07-2.150.25511450.19522791X-RAY DIFFRACTION99.83
2.15-2.230.2321550.17472777X-RAY DIFFRACTION99.76
2.23-2.340.25291620.17192810X-RAY DIFFRACTION99.93
2.34-2.460.20061220.18032828X-RAY DIFFRACTION99.9
2.46-2.610.19961350.18042833X-RAY DIFFRACTION99.97
2.61-2.810.21371320.17712842X-RAY DIFFRACTION99.83
2.81-3.10.23191410.17962834X-RAY DIFFRACTION99.63
3.1-3.550.22251470.16762819X-RAY DIFFRACTION98.83
3.55-4.470.18251450.1472905X-RAY DIFFRACTION100
4.47-63.950.20691620.16813006X-RAY DIFFRACTION99.15
Refinement TLS params.Method: refined / Origin x: -8.74778191482 Å / Origin y: -15.5228538415 Å / Origin z: 30.8028166791 Å
111213212223313233
T0.118323414022 Å20.00721961684243 Å2-0.0259128426327 Å2-0.146175300092 Å2-0.0151965701759 Å2--0.176874181357 Å2
L0.414578324622 °20.0537820368639 °20.019461663246 °2-1.47096477748 °2-0.670707479705 °2--1.19896365012 °2
S0.017068654386 Å °0.00915392032949 Å °0.0090691277309 Å °-0.136119796894 Å °0.057004057742 Å °0.159113300663 Å °0.139529760142 Å °-0.0907652260452 Å °-0.0321211730159 Å °
Refinement TLS groupSelection details: all

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