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- PDB-2vty: Vaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain sw... -

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Basic information

Entry
Database: PDB / ID: 2vty
TitleVaccinia virus anti-apoptotic F1L is a novel Bcl-2-like domain swapped dimer
ComponentsPROTEIN F1
KeywordsAPOPTOSIS / BCL-2 / VACCINIA VIRUS
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host apoptosis / regulation of apoptotic process / membrane
Similarity search - Function
Orthopoxvirus protein F1 / Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator OPG045
Similarity search - Component
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsKvansakul, M. / Yang, H. / Fairlie, W.D. / Czabotar, P.E. / Fischer, S.F. / Perugini, M.A. / Huang, D.C.S. / Colman, P.M.
CitationJournal: Cell Death Differ. / Year: 2008
Title: Vaccinia Virus Anti-Apoptotic F1L is a Novel Bcl-2-Like Domain-Swapped Dimer that Binds a Highly Selective Subset of Bh3-Containing Death Ligands.
Authors: Kvansakul, M. / Yang, H. / Fairlie, W.D. / Czabotar, P.E. / Fischer, S.F. / Perugini, M.A. / Huang, D.C.S. / Colman, P.M.
History
DepositionMay 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2May 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: PROTEIN F1


Theoretical massNumber of molelcules
Total (without water)21,4561
Polymers21,4561
Non-polymers00
Water1,18966
1
A: PROTEIN F1
x 12


Theoretical massNumber of molelcules
Total (without water)257,47512
Polymers257,47512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area58510 Å2
ΔGint-552.6 kcal/mol
Surface area69660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.261, 88.261, 88.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

#1: Protein PROTEIN F1 / F1L


Mass: 21456.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: MODIFIED VACCINIA ANKARA / Plasmid: PET DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: O57173
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HEXAHISTIDINE TAG PLUS LINKER SEQUENCE

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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: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 5.2 / Details: 0.9 NACL, 50 MM NA/K PHOSPHATE PH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 10, 2006 / Details: CAPILLARY OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13687 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9

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Processing

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

Resolution: 2.1→88.39 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.556 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 680 5 %RANDOM
Rwork0.192 ---
obs0.193 12940 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.971 Å2
Refinement stepCycle: LAST / Resolution: 2.1→88.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 0 66 1228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221199
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9671622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1645146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64123.14854
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95315224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2021510
X-RAY DIFFRACTIONr_chiral_restr0.1280.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02877
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.2505
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2855
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4620.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4692751
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59331191
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5714514
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8455429
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: 2.101→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 71
Rwork0.222 906

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