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- PDB-2i39: Crystal structure of Vaccinia virus N1L protein -

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Basic information

Entry
Database: PDB / ID: 2i39
TitleCrystal structure of Vaccinia virus N1L protein
ComponentsProtein N1
KeywordsVIRAL PROTEIN / All Alpha
Function / homology
Function and homology information


symbiont-mediated perturbation of host apoptosis / symbiont-mediated perturbation of host defense response / symbiont-mediated suppression of host NF-kappaB cascade
Similarity search - Function
Orthopoxvirus, Protein N1 / 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
Protein OPG035 / Protein OPG035
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsAoyagi, M. / Aleshin, A.E. / Stec, B. / Liddington, R.C.
CitationJournal: Protein Sci. / Year: 2007
Title: Vaccinia virus N1L protein resembles a B cell lymphoma-2 (Bcl-2) family protein.
Authors: Aoyagi, M. / Zhai, D. / Jin, C. / Aleshin, A.E. / Stec, B. / Reed, J.C. / Liddington, R.C.
History
DepositionAug 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Protein N1
B: Protein N1
C: Protein N1
D: Protein N1
E: Protein N1
F: Protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1338
Polymers96,8966
Non-polymers2362
Water5,080282
1
A: Protein N1
B: Protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4173
Polymers32,2992
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein N1
D: Protein N1


Theoretical massNumber of molelcules
Total (without water)32,2992
Polymers32,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Protein N1
F: Protein N1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4173
Polymers32,2992
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.640, 109.990, 69.580
Angle α, β, γ (deg.)90.00, 110.92, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains three dimers (A/B, C/D & E/F), which likely represent the biological assembly.

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Components

#1: Protein
Protein N1 / N1L protein


Mass: 16149.409 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Strain: Western Reserve / Gene: N1L (VACWR028) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P21054, UniProt: Q49PX0*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 4K, 0.1 M Tris HCl, 0.1 M sodium-potassium tartrate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2005
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 49469 / Num. obs: 47333 / % possible obs: 95.7 % / Observed criterion σ(I): 4 / Redundancy: 2.8 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3874 / Rsym value: 0.282 / % possible all: 79.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1498118.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2397 5.1 %RANDOM
Rwork0.202 ---
all-48947 --
obs-47043 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.3715 Å2 / ksol: 0.304499 e/Å3
Displacement parametersBiso mean: 40.864 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å25.7 Å2
2---1.01 Å20 Å2
3---3.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5879 0 0 298 6177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it2.562
X-RAY DIFFRACTIONc_scangle_it3.852.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 346 5 %
Rwork0.269 6641 -
obs--86.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4mpd.parammpd.top

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