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- PDB-4m0s: Crystal structure of Vaccinia virus protein A46 -

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Basic information

Entry
Database: PDB / ID: 4m0s
TitleCrystal structure of Vaccinia virus protein A46
ComponentsToll/IL1-receptor signalling interference protein A46
KeywordsVIRAL PROTEIN / BCl 2 fold / Toll/IL1-receptor signalling interference protein / protein binding
Function / homologydsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / Orthogonal Bundle / Mainly Alpha / Putative 27.6k protein / Putative 27.6k protein
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsChoe, J.W. / Kim, Y.W.
CitationJournal: To be Published
Title: Crystal structure of Vaccinia virus protein A46
Authors: Choe, J.W. / Kim, Y.W.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll/IL1-receptor signalling interference protein A46
B: Toll/IL1-receptor signalling interference protein A46


Theoretical massNumber of molelcules
Total (without water)34,1652
Polymers34,1652
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.242, 103.242, 313.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Toll/IL1-receptor signalling interference protein A46


Mass: 17082.533 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 79-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: Ankara / Gene: CVA180 / Production host: Escherichia coli (E. coli) / References: UniProt: A9J0Z8, UniProt: O57247*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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

Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.3M sodium formate, 0.1M Tris pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→26.79 Å / Num. obs: 29192

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→26.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.577 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23026 1564 5.1 %RANDOM
Rwork0.2004 ---
obs0.20187 29192 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.987 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.21 Å20 Å2
2---0.21 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.58→26.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 0 113 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192402
X-RAY DIFFRACTIONr_bond_other_d0.0020.022283
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9653237
X-RAY DIFFRACTIONr_angle_other_deg0.95135259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98123.86114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.58215447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.7941514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022649
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 95 -
Rwork0.347 2171 -
obs--98.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1696-0.4435-1.08460.97710.6862.7110.19410.24610.1956-0.14660.0438-0.0375-0.22560.0132-0.23780.30660.03480.01750.5485-0.05860.034630.21753.821161.649
22.7443-0.2665-2.16830.96420.32382.83780.2552-0.0570.17380.034-0.0672-0.0425-0.3119-0.1753-0.18810.2933-0.02610.03160.6036-0.0350.017358.52650.799148.163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 220
2X-RAY DIFFRACTION2B79 - 224

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