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- PDB-4d5s: Structure of A49 from Vaccinia Virus Western Reserve -

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Basic information

Entry
Database: PDB / ID: 4d5s
TitleStructure of A49 from Vaccinia Virus Western Reserve
ComponentsA49R
KeywordsVIRAL PROTEIN / POXVIRUS / B CELL LYMPHOMA 2 (BCL-2) FAMILY / INNATE IMMUNE MODULATOR / NUCLEAR FACTOR KAPPA B (NF-KB)
Function / homologyOrthopoxvirus A49 / Orthopoxvirus A49R protein / protein sequestering activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / host cell nucleus / Protein A49R
Function and homology information
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNeidel, S. / Maluquer de Motes, C. / Mansur, D.S. / Strnadova, P. / Smith, G.L. / Graham, S.C.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Vaccinia Virus Protein A49 is an Unexpected Member of the B-Cell Lymphoma (Bcl)-2 Protein Family
Authors: Neidel, S. / Maluquer De Motes, C. / Mansur, D.S. / Strnadova, P. / Smith, G.L. / Graham, S.C.
History
DepositionNov 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 1.4May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / 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 / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A49R
B: A49R


Theoretical massNumber of molelcules
Total (without water)39,4822
Polymers39,4822
Non-polymers00
Water00
1
B: A49R

B: A49R


Theoretical massNumber of molelcules
Total (without water)39,4822
Polymers39,4822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1500 Å2
ΔGint-12.8 kcal/mol
Surface area13750 Å2
MethodPISA
2
A: A49R

A: A49R


Theoretical massNumber of molelcules
Total (without water)39,4822
Polymers39,4822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1520 Å2
ΔGint-12.7 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.783, 67.783, 153.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein A49R


Mass: 19741.240 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: POPINE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P31037
Has protein modificationY
Sequence detailsCARRIES C-TERMINAL KH6 PURIFICATION TAG

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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: 2.22 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growTemperature: 294 K
Details: FULL-LENGTH A49 (100 NL AT 9.5 MG/ML) WAS MIXED WITH 100 NL RESERVOIR SOLUTION AND EQUILIBRATED AT 21 C AGAINST 95 UL RESERVOIRS COMPRISING 25% (WT/VOL) PEG 3350, 0.2 M AMMONIUM SULFATE AND ...Details: FULL-LENGTH A49 (100 NL AT 9.5 MG/ML) WAS MIXED WITH 100 NL RESERVOIR SOLUTION AND EQUILIBRATED AT 21 C AGAINST 95 UL RESERVOIRS COMPRISING 25% (WT/VOL) PEG 3350, 0.2 M AMMONIUM SULFATE AND 0.1 M TRIS PH 9.5. CRYOPROTECTION WAS ACHIEVED BY QUICKLY SWEEPING THE CRYSTAL THROUGH RESERVOIR SUPPLEMENTED WITH 20% (VOL/VOL) GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2008 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND (ASYMMETRIC LAUE 001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7353 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Biso Wilson estimate: 81.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D5R

4d5r


Resolution: 3→153.95 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 59.53 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27332 356 4.6 %RANDOM
Rwork0.21987 ---
obs0.22215 7350 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.958 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2--2.09 Å20 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 3→153.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 0 0 2292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022318
X-RAY DIFFRACTIONr_bond_other_d0.0030.022222
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9633146
X-RAY DIFFRACTIONr_angle_other_deg0.83235100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7145284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.25426.61118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022628
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02496
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_it3.6115.7591142
X-RAY DIFFRACTIONr_mcbond_other3.6055.761141
X-RAY DIFFRACTIONr_mcangle_it5.7828.6291424
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1266.1821176
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 24 -
Rwork0.358 532 -
obs--99.82 %
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)
18.25941.9435-1.30713.69340.14263.20090.64860.13650.12070.4755-0.42490.275-0.1054-0.0881-0.22370.43350.14270.0890.1998-0.02180.052814.22422.37214.216
27.94752.86060.6184.30540.60653.31290.69740.11520.46140.9064-0.47070.48920.40620.1193-0.22660.63740.09910.15570.1666-0.02860.1008-20.982-11.73813.899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 160
2X-RAY DIFFRACTION2B18 - 160

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