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- PDB-4d5r: Structure of N-terminally truncated A49 from Vaccinia Virus Weste... -

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Basic information

Entry
Database: PDB / ID: 4d5r
TitleStructure of N-terminally truncated A49 from Vaccinia Virus Western Reserve
ComponentsA49
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 / symbiont-mediated suppression of host NF-kappaB cascade / protein sequestering activity / host cell cytoplasm / host cell nucleus / Protein A49R
Function and homology information
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 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 / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.5May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A49
B: A49


Theoretical massNumber of molelcules
Total (without water)37,2802
Polymers37,2802
Non-polymers00
Water1,53185
1
A: A49


Theoretical massNumber of molelcules
Total (without water)18,6401
Polymers18,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A49


Theoretical massNumber of molelcules
Total (without water)18,6401
Polymers18,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.850, 42.740, 67.190
Angle α, β, γ (deg.)90.00, 100.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein A49


Mass: 18640.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 13-162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: POPTNH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P31037
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL 12 AMINO ACIDS REMOVED TO PROMOTE CRYSTALLISATION, CARRIES C-TERMINAL GSKH6 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: 2.16 Å3/Da / Density % sol: 43.1 % / Description: NONE
Crystal growTemperature: 293 K
Details: CRYSTALS WERE GROWN BY MIXING 2 UL PROTEIN (20-21 MG/ML) WITH 2 UL RESERVOIR SOLUTION AND EQUILIBRATING AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 1.3- 1.5 M SODIUM MALONATE PH 6.8, 1% ...Details: CRYSTALS WERE GROWN BY MIXING 2 UL PROTEIN (20-21 MG/ML) WITH 2 UL RESERVOIR SOLUTION AND EQUILIBRATING AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 1.3- 1.5 M SODIUM MALONATE PH 6.8, 1% (VOL/VOL) PEG 400 AND 4-10% (VOL/VOL) GLYCEROL, THE BEST CRYSTALS BEING OBTAINED WHEN THE RESERVOIR WAS OVERLAID WITH 100 UL OF A 1:1 MIXTURE OF PARAFFIN AND SILICONE OIL (MOLECULAR DIMENSIONS). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN 2.1 M SODIUM MALONATE, 1% (VOL/VOL) PEG 400 AND 5% (VOL/VOL) GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 19, 2013 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→33 Å / Num. obs: 25211 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 32.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.15 / Mean I/σ(I) obs: 2.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.9→33.03 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 11.038 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1279 5.1 %RANDOM
Rwork0.18521 ---
obs0.18735 23928 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.597 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-0.3 Å2
2--5.38 Å20 Å2
3----3.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 0 85 2484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192479
X-RAY DIFFRACTIONr_bond_other_d0.0070.022370
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9583373
X-RAY DIFFRACTIONr_angle_other_deg1.23935446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96726.142127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08615455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0131510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022845
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02549
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_it3.5483.7641217
X-RAY DIFFRACTIONr_mcbond_other3.5453.7611216
X-RAY DIFFRACTIONr_mcangle_it4.5275.6171527
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.5184.2271262
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 89 -
Rwork0.298 1744 -
obs--98.6 %
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)
13.071-1.33110.71212.352-0.33721.87660.023-0.10380.18170.2722-0.0857-0.0774-0.1297-0.2510.06270.1194-0.0612-0.040.305-0.02710.0494-21.5311.891-7.362
21.17740.38530.95132.56132.02115.48360.10240.245-0.14930.07180.1983-0.37390.23060.5157-0.30070.03770.0487-0.05640.34260.01470.1591-2.768-13.387-27.679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 163
2X-RAY DIFFRACTION2B17 - 163

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