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- PDB-4d5t: Structure of N-terminally truncated A49 from Vaccinia Virus Weste... -

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Basic information

Entry
Database: PDB / ID: 4d5t
TitleStructure of N-terminally truncated A49 from Vaccinia Virus Western Reserve
ComponentsPROTEIN A49R
KeywordsVIRAL PROTEIN / POX VIRUS / 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 / : / host cell cytoplasm / host cell nucleus / Protein A49R
Function and homology information
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 1.2Aug 12, 2015Group: Database references
Revision 1.3May 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 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
A: PROTEIN A49R
B: PROTEIN A49R
C: PROTEIN A49R
D: PROTEIN A49R
E: PROTEIN A49R
F: PROTEIN A49R
G: PROTEIN A49R
H: PROTEIN A49R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,60213
Polymers149,1218
Non-polymers4805
Water16,105894
1
A: PROTEIN A49R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7362
Polymers18,6401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN A49R


Theoretical massNumber of molelcules
Total (without water)18,6401
Polymers18,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN A49R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7362
Polymers18,6401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROTEIN A49R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7362
Polymers18,6401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PROTEIN A49R


Theoretical massNumber of molelcules
Total (without water)18,6401
Polymers18,6401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PROTEIN A49R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7362
Polymers18,6401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PROTEIN A49R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7362
Polymers18,6401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: PROTEIN A49R


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)92.290, 45.630, 160.260
Angle α, β, γ (deg.)90.00, 98.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN A49R / A49


Mass: 18640.160 Da / Num. of mol.: 8
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): ROSETTA PLYSS / References: UniProt: P31037
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 894 / 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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growTemperature: 293 K
Details: PROTEIN (1 UL AT 25.0 MG/ML) WAS MIXED WITH 1 UL RESERVOIR SOLUTION AND EQUILIBRATED AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 0.1 M HEPES PH 7.5, 1.6 M AMMONIUM SULFATE AND 1.5% (VOL/VOL) ...Details: PROTEIN (1 UL AT 25.0 MG/ML) WAS MIXED WITH 1 UL RESERVOIR SOLUTION AND EQUILIBRATED AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 0.1 M HEPES PH 7.5, 1.6 M AMMONIUM SULFATE AND 1.5% (VOL/VOL) PEG 400. CRYSTALS WERE CRYOPROTECTED BY PASSAGE THROUGH 2 UL OF PERFLUOROPOLYETHER OIL (HAMPTON RESEARCH) THAT HAD BEEN OVERLAID ONTO THE MOTHER LIQUOR.

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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: Mar 2, 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: 1.84→45.7 Å / Num. obs: 112855 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.16 / Mean I/σ(I) obs: 1.5 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D5R

4d5r


Resolution: 1.84→45.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.18 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.23888 5665 5 %RANDOM
Rwork0.20638 ---
obs0.20801 107126 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.864 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å20 Å20.82 Å2
2--0.49 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9714 0 25 894 10633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0210287
X-RAY DIFFRACTIONr_bond_other_d0.0140.029724
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.96214047
X-RAY DIFFRACTIONr_angle_other_deg1.988322393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50951302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48226.415530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.285151876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8981539
X-RAY DIFFRACTIONr_chiral_restr0.1040.21683
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211984
X-RAY DIFFRACTIONr_gen_planes_other0.010.022267
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_it2.062.1435070
X-RAY DIFFRACTIONr_mcbond_other2.062.1425069
X-RAY DIFFRACTIONr_mcangle_it2.8683.1996409
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9982.4785217
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: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 414 -
Rwork0.332 7671 -
obs--95.68 %
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)
11.8277-0.2316-0.01121.124-0.3311.29250.0185-0.0961-0.0210.16160.01180.1478-0.0477-0.0466-0.03030.14090.00960.01940.0656-0.05090.06783.3401-0.314938.6191
23.41970.3897-0.24231.50210.26771.0181-0.00930.09770.3887-0.21120.0903-0.1113-0.0714-0.0029-0.0810.14850.00390.01130.0920.05050.091236.376-20.53350.6253
32.12960.2749-0.43910.79450.3111.29230.0170.2270.0137-0.1304-0.0249-0.1107-0.0407-0.02270.00790.10960.00490.01310.05710.01580.021924.224820.004579.9381
44.48720.2323-0.45530.85580.29581.20830.08460.17980.5628-0.1786-0.0383-0.0569-0.1023-0.0438-0.04630.12130.03090.02710.0414-0.00180.123-15.982-23.083640.1091
53.12680.74330.01051.639-0.55081.7020.12530.1409-0.2603-0.1218-0.1274-0.10230.14250.05320.00210.1360.0291-0.03070.0404-0.02210.039249.17065.548141.8174
62.02920.694-0.38881.9985-1.12341.9942-0.06760.24780.0185-0.246-0.0333-0.10370.2406-0.04480.10090.1389-0.0191-0.03380.07520.0320.06139.33838.08122.3308
73.21681.4133-0.672.6323-0.74651.3140.1451-0.0891-0.1834-0.0548-0.2463-0.04220.11790.07280.10120.0909-0.0068-0.01930.07010.00130.0209-2.64552.428880.9496
82.7576-1.3323-0.6932.42360.8971.36430.0473-0.077-0.21660.1223-0.12110.03830.15750.01040.07380.14430.0433-0.05390.08090.01170.103630.4853-17.75237.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 163
2X-RAY DIFFRACTION2B13 - 163
3X-RAY DIFFRACTION3C13 - 162
4X-RAY DIFFRACTION4D13 - 163
5X-RAY DIFFRACTION5E13 - 163
6X-RAY DIFFRACTION6F13 - 162
7X-RAY DIFFRACTION7G13 - 162
8X-RAY DIFFRACTION8H13 - 162

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