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- PDB-4lqk: Structure of the vaccinia virus NF- B antagonist A46 -

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Basic information

Entry
Database: PDB / ID: 4lqk
TitleStructure of the vaccinia virus NF- B antagonist A46
ComponentsProtein A46
KeywordsVIRAL PROTEIN / Bcl-2-like fold
Function / homology
Function and homology information


extrinsic component of cytoplasmic side of plasma membrane / protein sequestering activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated suppression of host NF-kappaB cascade
Similarity search - Function
dsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / Protein OPG176
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsGrishkovskaya, I. / Fedosyuk, S. / Skern, T. / Djinovic-Carugo, K.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Characterization and Structure of the Vaccinia Virus NF-kappa B Antagonist A46.
Authors: Fedosyuk, S. / Grishkovskaya, I. / de Almeida Ribeiro, E. / Skern, T.
History
DepositionJul 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Protein A46
D: Protein A46
A: Protein A46
B: Protein A46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1567
Polymers67,0304
Non-polymers1263
Water4,125229
1
C: Protein A46
D: Protein A46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5383
Polymers33,5152
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-13 kcal/mol
Surface area13130 Å2
MethodPISA
2
A: Protein A46
B: Protein A46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6184
Polymers33,5152
Non-polymers1032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-16 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.114, 107.633, 137.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-409-

HOH

21D-436-

HOH

31B-412-

HOH

41B-442-

HOH

Details2 dimers molecules present in asymmetric unit between monomers C and D; and A and B

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Components

#1: Protein
Protein A46


Mass: 16757.527 Da / Num. of mol.: 4 / Fragment: UNP residues 87-229 / Mutation: C205S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Western Reserve / Gene: VACWR172, A46R / Production host: Escherichia coli (E. coli) / References: UniProt: P26672
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM bis-tris-propane pH 7.5, 150 mM NaBr, 18% PEG3350, VAPOR DIFFUSION, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2013
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.99→75.924 Å / Num. all: 54679 / Num. obs: 54421 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.163 / Net I/σ(I): 10.4
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.809 / Mean I/σ(I) obs: 1.3 / Num. unique all: 3762 / % possible all: 92.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.7.0032refinement
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.99→42.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.731 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21872 2759 5.1 %RANDOM
Rwork0.1969 ---
obs0.19803 51639 99.48 %-
all-54679 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0 Å2
2---0.22 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.99→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 3 229 4584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0080.0194549
X-RAY DIFFRACTIONf_bond_other_d0.0010.024391
X-RAY DIFFRACTIONf_angle_refined_deg1.2021.9776152
X-RAY DIFFRACTIONf_angle_other_deg0.749310134
X-RAY DIFFRACTIONf_dihedral_angle_1_deg4.675570
X-RAY DIFFRACTIONf_dihedral_angle_2_deg34.26923.704216
X-RAY DIFFRACTIONf_dihedral_angle_3_deg13.91215829
X-RAY DIFFRACTIONf_dihedral_angle_4_deg19.0211531
X-RAY DIFFRACTIONf_chiral_restr0.0650.2697
X-RAY DIFFRACTIONf_gen_planes_refined0.0040.025064
X-RAY DIFFRACTIONf_gen_planes_other0.0010.021063
X-RAY DIFFRACTIONf_nbd_refined
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it1.6862.9212175
X-RAY DIFFRACTIONf_mcbond_other1.6842.922174
X-RAY DIFFRACTIONf_mcangle_it2.6414.372723
X-RAY DIFFRACTIONf_mcangle_other2.6414.3712724
X-RAY DIFFRACTIONf_scbond_it2.1753.1672374
X-RAY DIFFRACTIONf_scbond_other2.1743.1652372
X-RAY DIFFRACTIONf_scangle_it
X-RAY DIFFRACTIONf_scangle_other3.4894.6443410
X-RAY DIFFRACTIONf_long_range_B_refined5.01523.3775541
X-RAY DIFFRACTIONf_long_range_B_other4.93123.2465496
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 159 -
Rwork0.31 3577 -
obs--93.59 %

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