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- PDB-2vvw: Structure of Vaccinia virus protein A52 -

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Basic information

Entry
Database: PDB / ID: 2vvw
TitleStructure of Vaccinia virus protein A52
ComponentsPROTEIN A52
KeywordsVIRAL PROTEIN / IRAK2 / TRAF6 / BCL-2 FAMILY / VACCINIA VIRUS / IMMUNOMODULATOR / NF-KB ACTIVATION / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated suppression of host TRAF-mediated signal transduction / protein sequestering activity / host cell cytoplasm / virus-mediated perturbation of host defense response
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
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsGraham, S.C. / Bahar, M.W. / Cooray, S. / Chen, R.A.-J. / Whalen, D.M. / Abrescia, N.G.A. / Alderton, D. / Owens, R.J. / Stuart, D.I. / Smith, G.L. / Grimes, J.M.
CitationJournal: Plos Pathog. / Year: 2008
Title: Vaccinia Virus Proteins A52 and B14 Share a Bcl-2-Like Fold But Have Evolved to Inhibit NF-kappaB Rather Than Apoptosis
Authors: Graham, S.C. / Bahar, M.W. / Cooray, S. / Chen, R.A.-J. / Whalen, D.M. / Abrescia, N.G.A. / Alderton, D. / Owens, R.J. / Stuart, D.I. / Smith, G.L. / Grimes, J.M.
History
DepositionJun 12, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN A52
B: PROTEIN A52


Theoretical massNumber of molelcules
Total (without water)39,1792
Polymers39,1792
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7.4 kcal/mol
Surface area18220 Å2
MethodPQS
2
A: PROTEIN A52


Theoretical massNumber of molelcules
Total (without water)19,5901
Polymers19,5901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: PROTEIN A52


Theoretical massNumber of molelcules
Total (without water)19,5901
Polymers19,5901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.208, 59.144, 75.719
Angle α, β, γ (deg.)90.00, 106.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN A52 / A52


Mass: 19589.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) PLYSS / References: UniProt: Q01220
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-36 ARE REMOVED, AN N-TERMINAL START CODON IS ADDED AND A C-TERMINAL LYS-HIS6 ...RESIDUES 1-36 ARE REMOVED, AN N-TERMINAL START CODON IS ADDED AND A C-TERMINAL LYS-HIS6 PURIFICATION TAG IS ADDED.

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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: 2.55 Å3/Da / Density % sol: 51.84 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: HANGING DROPS CONTAINING 1 UL PROTEIN (5.3 MG/ML IN 20 MM TRIS, 200 MM NACL, PH 7.5) AND 1 UL RESERVOIR SOLUTION (0.2 M TRISODIUM CITRATE, 18% (W/V) PEG 3350) WERE EQUILIBRATED AGAINST 500 ...Details: HANGING DROPS CONTAINING 1 UL PROTEIN (5.3 MG/ML IN 20 MM TRIS, 200 MM NACL, PH 7.5) AND 1 UL RESERVOIR SOLUTION (0.2 M TRISODIUM CITRATE, 18% (W/V) PEG 3350) WERE EQUILIBRATED AGAINST 500 UL RESERVOIRS AT 21 C. CRYSTALS WERE CRYOPROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 20% (V/V) GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 27, 2007 / Details: MIRRORS
RadiationMonochromator: SILICON (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30971 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 24.16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→33.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.892 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1571 5.1 %RANDOM
Rwork0.177 ---
obs0.179 29385 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å2-0.84 Å2
2---0.75 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 0 207 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222591
X-RAY DIFFRACTIONr_bond_other_d0.0010.021822
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.9753484
X-RAY DIFFRACTIONr_angle_other_deg0.83434435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19724.485136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42115521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5081518
X-RAY DIFFRACTIONr_chiral_restr0.0680.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02544
X-RAY DIFFRACTIONr_nbd_refined0.2090.2558
X-RAY DIFFRACTIONr_nbd_other0.1730.21831
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21279
X-RAY DIFFRACTIONr_nbtor_other0.0820.21321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3450.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.37121644
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87332430
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.83241226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.12361050
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 86
Rwork0.252 2161
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)
10.91880.21250.28021.86210.29583.40550.0301-0.0406-0.03490.0969-0.0032-0.0980.27420.0004-0.0269-0.15130.01050.0103-0.11960.001-0.111935.884-13.59912.451
21.6328-0.56541.06282.06370.13642.8993-0.1016-0.0630.09540.08280.0736-0.0976-0.17270.02530.028-0.1367-0.03140.0269-0.1165-0.0116-0.129436.78714.42618.866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 190
2X-RAY DIFFRACTION2B40 - 190

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