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- PDB-5hx4: Zinc-Free APOBEC3F Catalytic Domain Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 5hx4
TitleZinc-Free APOBEC3F Catalytic Domain Crystal Structure
ComponentsDNA dC->dU-editing enzyme APOBEC-3F
KeywordsHYDROLASE / APOBEC3F
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 dC->dU-editing enzyme APOBEC-3F
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsShaban, N.M. / Shi, K. / Aihara, H. / Harris, R.S.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: 1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure.
Authors: Shaban, N.M. / Shi, K. / Li, M. / Aihara, H. / Harris, R.S.
History
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine / struct_ref_seq_dif
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA dC->dU-editing enzyme APOBEC-3F
B: DNA dC->dU-editing enzyme APOBEC-3F


Theoretical massNumber of molelcules
Total (without water)46,7222
Polymers46,7222
Non-polymers00
Water2,108117
1
A: DNA dC->dU-editing enzyme APOBEC-3F


Theoretical massNumber of molelcules
Total (without water)23,3611
Polymers23,3611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA dC->dU-editing enzyme APOBEC-3F


Theoretical massNumber of molelcules
Total (without water)23,3611
Polymers23,3611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.100, 51.270, 99.770
Angle α, β, γ (deg.)90.00, 90.85, 90.00
Int Tables number4
Space group name H-MP1211

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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: 23361.082 Da / Num. of mol.: 2 / Fragment: UNP residues 185-373
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.98 Å3/Da / Density % sol: 37.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tacsimate pH5.0, PEG3350, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→49.91 Å / Num. obs: 25900 / % possible obs: 96 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.1
Reflection shellResolution: 1.92→2 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 0.8 / % possible all: 62.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2356: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IOU

4iou


Resolution: 1.92→36.096 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1299 5.02 %
Rwork0.1848 --
obs0.1863 24630 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→36.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 0 117 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113018
X-RAY DIFFRACTIONf_angle_d0.9514101
X-RAY DIFFRACTIONf_dihedral_angle_d14.2351740
X-RAY DIFFRACTIONf_chiral_restr0.059404
X-RAY DIFFRACTIONf_plane_restr0.008531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.99690.31691050.31371959X-RAY DIFFRACTION67
1.9969-2.08780.3321260.28332395X-RAY DIFFRACTION82
2.0878-2.19780.31811500.25982849X-RAY DIFFRACTION97
2.1978-2.33550.25971540.22972900X-RAY DIFFRACTION98
2.3355-2.51580.24311540.21242880X-RAY DIFFRACTION98
2.5158-2.76890.27171550.20942936X-RAY DIFFRACTION99
2.7689-3.16930.24761460.19092921X-RAY DIFFRACTION98
3.1693-3.99220.1961560.1632890X-RAY DIFFRACTION97
3.9922-36.10240.15711530.14812871X-RAY DIFFRACTION94

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