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- PDB-5k81: Crystal Structure of a Primate APOBEC3G N-Terminal Domain -

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Basic information

Entry
Database: PDB / ID: 5k81
TitleCrystal Structure of a Primate APOBEC3G N-Terminal Domain
ComponentsApolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
KeywordsHYDROLASE / APOBEC3G / Vif / HIV / APOBEC
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / DNA cytosine deamination / deoxycytidine deaminase activity / cytidine deaminase activity / retrotransposon silencing / P-body / defense response to virus / ribonucleoprotein complex / innate immune response / zinc ion binding / nucleus
Similarity search - Function
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-3G
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.006 Å
AuthorsXiao, X. / Li, S.-X. / Yang, H. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087986 United States
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structures of APOBEC3G N-domain alone and its complex with DNA.
Authors: Xiao, X. / Li, S.X. / Yang, H. / Chen, X.S.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
B: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
C: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
D: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
E: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
F: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,94912
Polymers138,5576
Non-polymers3926
Water11,566642
1
A: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
F: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3164
Polymers46,1862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-89 kcal/mol
Surface area19150 Å2
MethodPISA
2
B: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
D: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3164
Polymers46,1862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-89 kcal/mol
Surface area19220 Å2
MethodPISA
3
C: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
E: Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3164
Polymers46,1862
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-91 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.213, 81.297, 106.298
Angle α, β, γ (deg.)90.00, 120.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G,Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G


Mass: 23092.783 Da / Num. of mol.: 6
Fragment: UNP residues 1-195 (139CQKRDGPH146 replaced by AEAG)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: APOBEC3G / Plasmid: pGEX-6P-1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: M1GSK9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na K tartrate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2→46.014 Å / Num. obs: 102317 / % possible obs: 97.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.5 / % possible all: 82.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J4J

4j4j


Resolution: 2.006→46.014 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1966 1.98 %
Rwork0.1877 --
obs0.1884 99525 94.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.006→46.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9493 0 6 642 10141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099826
X-RAY DIFFRACTIONf_angle_d1.13713352
X-RAY DIFFRACTIONf_dihedral_angle_d12.7633633
X-RAY DIFFRACTIONf_chiral_restr0.0491357
X-RAY DIFFRACTIONf_plane_restr0.0061686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0064-2.05660.2966990.26824880X-RAY DIFFRACTION67
2.0566-2.11220.31220.23186070X-RAY DIFFRACTION83
2.1122-2.17430.23871340.21166790X-RAY DIFFRACTION93
2.1743-2.24450.20131340.20156971X-RAY DIFFRACTION96
2.2445-2.32470.21561440.19787146X-RAY DIFFRACTION97
2.3247-2.41780.26351460.21187165X-RAY DIFFRACTION98
2.4178-2.52780.28511550.2127195X-RAY DIFFRACTION98
2.5278-2.66110.24191410.21167221X-RAY DIFFRACTION99
2.6611-2.82780.23091470.20337225X-RAY DIFFRACTION99
2.8278-3.04610.24921550.20097334X-RAY DIFFRACTION99
3.0461-3.35260.27151420.19057349X-RAY DIFFRACTION100
3.3526-3.83750.21941440.18567346X-RAY DIFFRACTION100
3.8375-4.8340.17271470.15477426X-RAY DIFFRACTION100
4.834-46.02560.19321560.16437441X-RAY DIFFRACTION99

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