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

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Basic information

Entry
Database: PDB / ID: 6wmb
TitleCrystal structure of a soluble variant of full-length human APOBEC3G (pH 8.0)
Components
  • APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC PEPTIDE- LIKE 3G
  • DNA (5'-D(P*CP*C)-3')
KeywordsHYDROLASE/DNA / APOBEC3G / ANTIVIRAL DEFENSE / HYDROLASE / DNA CYTIDINE DEAMINASE / HYDROLASE-DNA complex
Function / homologyCytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / DNA
Function and homology information
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 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- 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
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.238, 42.081, 194.210
Angle α, β, γ (deg.)90.000, 95.759, 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- 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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris (pH 8.0) and 5.5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.02→40 Å / Num. obs: 7726 / % possible obs: 84.1 % / Redundancy: 2.7 % / Biso Wilson estimate: 72.85 Å2 / CC1/2: 0.942 / Rmerge(I) obs: 0.183 / Net I/σ(I): 5.17
Reflection shellResolution: 3.02→3.21 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 367 / CC1/2: 0.498 / % possible all: 79.2

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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: 3.02→35.23 Å / SU ML: 0.5058 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.2455
RfactorNum. reflection% reflection
Rfree0.3046 775 10.03 %
Rwork0.2467 --
obs0.2526 7726 78.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.01 Å2
Refinement stepCycle: LAST / Resolution: 3.02→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 38 1 46 2960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00182997
X-RAY DIFFRACTIONf_angle_d0.41924074
X-RAY DIFFRACTIONf_chiral_restr0.037425
X-RAY DIFFRACTIONf_plane_restr0.0034526
X-RAY DIFFRACTIONf_dihedral_angle_d12.75221744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.20.3411900.2966780X-RAY DIFFRACTION53.57
3.2-3.450.41921390.30911251X-RAY DIFFRACTION85.86
3.45-3.80.3367870.2964798X-RAY DIFFRACTION54.33
3.8-4.350.27181380.24931237X-RAY DIFFRACTION84.93
4.35-5.470.28351580.21421427X-RAY DIFFRACTION96.53
5.47-35.230.29351630.23491458X-RAY DIFFRACTION94.63

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