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- PDB-5w2m: APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA -

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Basic information

Entry
Database: PDB / ID: 5w2m
TitleAPOBEC3F Catalytic Domain Complex with a Single-Stranded DNA
Components
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • DNA dC->dU-editing enzyme APOBEC-3F
KeywordsDNA BINDING PROTEIN / APOBEC
Function / homology
Function and homology information


apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of viral process / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate ...apolipoprotein B mRNA editing enzyme complex / base conversion or substitution editing / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / clearance of foreign intracellular DNA / negative regulation of viral process / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / positive regulation of gene expression via chromosomal CpG island demethylation / retrotransposon silencing / negative regulation of viral genome replication / positive regulation of defense response to virus by host / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
APOBEC-like N-terminal domain / 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
DNA / DNA dC->dU-editing enzyme APOBEC-3F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsFang, Y. / Xiao, X. / Li, S.-X. / Wolfe, A. / Chen, X.S.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Molecular Interactions of a DNA Modifying Enzyme APOBEC3F Catalytic Domain with a Single-Stranded DNA.
Authors: Fang, Y. / Xiao, X. / Li, S.X. / Wolfe, A. / Chen, X.S.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2
Item: _audit_author.name / _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: DNA dC->dU-editing enzyme APOBEC-3F
B: DNA dC->dU-editing enzyme APOBEC-3F
C: DNA dC->dU-editing enzyme APOBEC-3F
D: DNA dC->dU-editing enzyme APOBEC-3F
E: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
J: DNA dC->dU-editing enzyme APOBEC-3F
K: DNA dC->dU-editing enzyme APOBEC-3F
L: DNA dC->dU-editing enzyme APOBEC-3F
M: DNA dC->dU-editing enzyme APOBEC-3F
N: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,39914
Polymers183,13710
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15700 Å2
ΔGint-232 kcal/mol
Surface area74500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.194, 108.489, 108.549
Angle α, β, γ (deg.)79.600, 71.800, 71.750
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA dC->dU-editing enzyme APOBEC-3F / Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F / A3F


Mass: 22142.910 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3F / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IUX4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2996.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05 M HEPES, pH 7.0, 0.1 M Potassium chloride, 0.005 M Magnesium Sulfate, 15%(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 29144 / % possible obs: 96.2 % / Redundancy: 2.8 % / Net I/σ(I): 4.7

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Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2666 2866 9.6 %
Rwork0.2498 25887 -
obs-28753 96.4 %
Solvent computationBsol: 32.0874 Å2
Displacement parametersBiso max: 225.46 Å2 / Biso mean: 107.8855 Å2 / Biso min: 71.34 Å2
Baniso -1Baniso -2Baniso -3
1-19.273 Å2-4.636 Å21.885 Å2
2---5.957 Å23.075 Å2
3----13.316 Å2
Refinement stepCycle: final / Resolution: 3.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12520 402 4 0 12926
Biso mean--223.62 --
Num. residues----1492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.102
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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