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- PDB-2vvy: Structure of Vaccinia virus protein B14 -

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Basic information

Entry
Database: PDB / ID: 2vvy
TitleStructure of Vaccinia virus protein B14
ComponentsPROTEIN B15
KeywordsVIRAL PROTEIN / IKK / IKK BETA / BCL-2 FAMILY / EARLY PROTEIN / HOST-VIRUS INTERACTION / VACCINIA VIRUS / IMMUNOMODULATOR / NF-KB ACTIVATION
Function / homology
Function and homology information


Poxvirus, Protein B14/B22/C16 / 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: 2.693 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 / 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.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN B15
B: PROTEIN B15
C: PROTEIN B15
D: PROTEIN B15


Theoretical massNumber of molelcules
Total (without water)79,4024
Polymers79,4024
Non-polymers00
Water00
1
A: PROTEIN B15
C: PROTEIN B15


Theoretical massNumber of molelcules
Total (without water)39,7012
Polymers39,7012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-13.7 kcal/mol
Surface area15690 Å2
MethodPQS
2
B: PROTEIN B15
D: PROTEIN B15


Theoretical massNumber of molelcules
Total (without water)39,7012
Polymers39,7012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-10.9 kcal/mol
Surface area15560 Å2
MethodPQS
Unit cell
Length a, b, c (Å)168.673, 43.884, 99.878
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B AND NOT (RESID 1:9 OR RESID 27:28 OR RESID 42:45 OR RESID 117:120 )
311CHAIN C AND NOT (RESID 1:9 OR RESID 27:28 OR RESID 42:45 OR RESID 117:120 )
411CHAIN D AND NOT (RESID 1:9 OR RESID 27:28 OR RESID 42:45 OR RESID 117:120 )

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Components

#1: Protein
PROTEIN B15 / B14


Mass: 19850.463 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P24772
Sequence detailsTHE ADDED N-TERMINAL HIS6 FUSION TAG AND THROMBIN CLEAVAGE SITE ARISE FROM THE PET-28A EXPRESSION VECTOR.

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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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: SITTING DROPS CONTAINING 100 NL PROTEIN (3.2 MG/ML IN 50 MM TRIS PH 8.5, 150 MM NACL, 2 MM 2-MERCAPTOETHANOL) AND 100 NL RESERVOIR SOLUTION (0.2 M DIAMMONIUM TARTRATE, 20% (W/V) PEG 3350, 0. ...Details: SITTING DROPS CONTAINING 100 NL PROTEIN (3.2 MG/ML IN 50 MM TRIS PH 8.5, 150 MM NACL, 2 MM 2-MERCAPTOETHANOL) AND 100 NL RESERVOIR SOLUTION (0.2 M DIAMMONIUM TARTRATE, 20% (W/V) PEG 3350, 0.4 M NON-DETERGENT SULPHOBETANE 201 AND 2 MM 2-MERCAPTOETHANOL) WERE EQUILIBRATED AGAINST 95 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: BM14 / Wavelength: 0.8856
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 8, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 19127 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 50.56 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2MAPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.693→46.273 Å / SU ML: 0.35 / Phase error: 28.66 / Stereochemistry target values: ML / Details: B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflection
Rfree0.2439 1783 4.9 %
Rwork0.2225 --
obs0.2236 36439 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.43 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1--10.5475 Å20 Å22.6113 Å2
2---8.2398 Å20 Å2
3---13.8357 Å2
Refinement stepCycle: LAST / Resolution: 2.693→46.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 0 0 4632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054744
X-RAY DIFFRACTIONf_angle_d0.7776440
X-RAY DIFFRACTIONf_dihedral_angle_d14.1631680
X-RAY DIFFRACTIONf_chiral_restr0.054700
X-RAY DIFFRACTIONf_plane_restr0.004828
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1051X-RAY DIFFRACTIONPOSITIONAL
12B1051X-RAY DIFFRACTIONPOSITIONAL0.029
13C1051X-RAY DIFFRACTIONPOSITIONAL0.026
14D1047X-RAY DIFFRACTIONPOSITIONAL0.028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6934-2.76620.4123990.38082577X-RAY DIFFRACTION94
2.7662-2.84760.4131250.36122659X-RAY DIFFRACTION100
2.8476-2.93950.35371670.33752713X-RAY DIFFRACTION100
2.9395-3.04450.28531700.30262600X-RAY DIFFRACTION100
3.0445-3.16640.24161260.27222689X-RAY DIFFRACTION100
3.1664-3.31040.27521390.25922709X-RAY DIFFRACTION100
3.3104-3.48490.28081610.24522653X-RAY DIFFRACTION100
3.4849-3.70320.29871440.22722691X-RAY DIFFRACTION100
3.7032-3.98890.23531620.19342659X-RAY DIFFRACTION100
3.9889-4.39010.17721210.16662716X-RAY DIFFRACTION100
4.3901-5.02470.1951110.15962679X-RAY DIFFRACTION100
5.0247-6.3280.19811070.18052711X-RAY DIFFRACTION99
6.328-46.27930.16461510.17162600X-RAY DIFFRACTION98
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)
11.095-0.1026-0.36642.0780.3120.64040.0264-0.13380.02560.0852-0.1448-0.12450.049-0.01790.08260.0422-0.050.03410.17760.00680.1204-40.08712.777612.7107
23.57251.0957-1.0984-0.3931-0.61581.6448-0.05690.0681-0.5158-0.0849-0.14090.01740.21760.03720.21280.29010.0556-0.11710.1429-0.02370.427-79.8836-2.753919.7358
33.52030.637-0.37850.0122-0.20622.1519-0.0942-0.2057-0.3994-0.13110.00330.09010.2067-0.09250.08490.24560.0315-0.06940.16630.03980.4462-20.8903-3.043525.5946
42.52580.08720.37490.8843-0.15273.2589-0.0150.055-0.0019-0.053-0.0692-0.0463-0.18960.04910.00360.20750.0349-0.03620.0886-0.01030.1211-62.014.210933.3564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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