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- PDB-6wmc: Crystal structure of a soluble variant of full-length human APOBE... -

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Basic information

Entry
Database: PDB / ID: 6wmc
TitleCrystal structure of a soluble variant of full-length human APOBEC3G (pH 9.0)
Components
  • APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE-3 LIKE 3G
  • DNA (5'-D(P*CP*C)-3')
KeywordsHYDROLASE/DNA / APOBEC3G / ANTIVIRAL DEFENSE / HYDROLASE / DNA CYTIDINE DEAMINASE / HYDROLASE-DNA complex
Function / homologyDNA
Function and homology information
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsMaiti, A. / Matsuo, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1AI150478 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Crystal Structure of a Soluble APOBEC3G Variant Suggests ssDNA to Bind in a Channel that Extends between the Two Domains.
Authors: Maiti, A. / Myint, W. / Delviks-Frankenberry, K.A. / Hou, S. / Kanai, T. / Balachandran, V. / Sierra Rodriguez, C. / Tripathi, R. / Kurt Yilmaz, N. / Pathak, V.K. / Schiffer, C.A. / Matsuo, H.
History
DepositionApr 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE-3 LIKE 3G
B: DNA (5'-D(P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0673
Polymers43,0012
Non-polymers651
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-39 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.233, 42.091, 191.911
Angle α, β, γ (deg.)90.000, 95.939, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE-3 LIKE 3G


Mass: 42467.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(P*CP*C)-3')


Mass: 533.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M BICINE (pH 9.0) and 10% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.49→50 Å / Num. obs: 5588 / % possible obs: 89 % / Redundancy: 2.8 % / Biso Wilson estimate: 69.24 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.08
Reflection shellResolution: 3.49→3.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 482 / CC1/2: 0.718 / % possible all: 83.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BUX CHAIN A AND 5K81 CHAIN A

6bux

5k81


Resolution: 3.49→47.72 Å / SU ML: 0.5317 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.896
RfactorNum. reflection% reflection
Rfree0.2742 559 10 %
Rwork0.2164 --
obs0.2222 5588 88.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.28 Å2
Refinement stepCycle: LAST / Resolution: 3.49→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 38 1 39 2999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243044
X-RAY DIFFRACTIONf_angle_d0.50774133
X-RAY DIFFRACTIONf_chiral_restr0.0386427
X-RAY DIFFRACTIONf_plane_restr0.003535
X-RAY DIFFRACTIONf_dihedral_angle_d11.97511777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.840.32511290.2751179X-RAY DIFFRACTION84.39
3.84-4.40.26831380.22121224X-RAY DIFFRACTION88.33
4.4-5.540.27271420.2041284X-RAY DIFFRACTION90.25
5.54-47.720.25581500.19661342X-RAY DIFFRACTION91.48

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