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

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Basic information

Entry
Database: PDB / ID: 6wma
TitleCrystal structure of a soluble variant of full-length human APOBEC3G (pH 7.6)
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: 2.5 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

Downloads & links

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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)43,1945
Polymers43,0012
Non-polymers1933
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-55 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 41.870, 191.541
Angle α, β, γ (deg.)90.000, 95.360, 90.000
Int Tables number5
Space group name H-MI121
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

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Protein / DNA chain , 2 types, 2 molecules AB

#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)

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Non-polymers , 4 types, 153 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.03 M Citric acid, 0.07 M BIS-TRIS propane (pH 7.6) and 20% w/v PEG 3350

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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: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→31.72 Å / Num. obs: 14930 / % possible obs: 90.1 % / Redundancy: 3 % / Biso Wilson estimate: 30.41 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1301 / CC1/2: 0.769 / % possible all: 80.8

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Processing

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

6bux

5k81


Resolution: 2.5→31.717 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 688 4.61 %
Rwork0.1969 14242 -
obs0.1993 14930 89.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.44 Å2 / Biso mean: 37.4646 Å2 / Biso min: 12.5 Å2
Refinement stepCycle: final / Resolution: 2.5→31.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 38 8 150 3112
Biso mean--48.63 34.83 -
Num. residues----363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5001-2.69310.2861350.2302260583
2.6931-2.96390.31271260.2452287190
2.9639-3.39240.29581360.2104290792
3.3924-4.27240.22661540.1804284889
4.2724-31.710.20281370.1747301191

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