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- PDB-2uxe: The structure of Vaccinia virus N1 -

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Basic information

Entry
Database: PDB / ID: 2uxe
TitleThe structure of Vaccinia virus N1
ComponentsHYPOTHETICAL PROTEIN
KeywordsVIRAL PROTEIN / BCL-LIKE PROTEIN / HYPOTHETICAL PROTEIN / VIRAL PROTEIN APOPTOSIS / VACCINIA VIRUS / VIRULENCE FACTOR
Function / homology
Function and homology information


symbiont-mediated perturbation of host apoptosis / virus-mediated perturbation of host defense response
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
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsCooray, S. / Bahar, M.W. / Abrescia, N.G.A. / McVey, C.E. / Bartlett, N.W. / Chen, R.A.-J. / Stuart, D.I. / Grimes, J.M. / Smith, G.L.
CitationJournal: J.Gen.Virol. / Year: 2007
Title: Functional and Structural Studies of the Vaccinia Virus Virulence Factor N1 Reveal a Bcl-2-Like Anti- Apoptotic Protein
Authors: Cooray, S. / Bahar, M.W. / Abrescia, N.G.A. / Mcvey, C.E. / Bartlett, N.W. / Chen, R.A.-J. / Stuart, D.I. / Grimes, J.M. / Smith, G.L.
History
DepositionMar 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN
B: HYPOTHETICAL PROTEIN
C: HYPOTHETICAL PROTEIN
D: HYPOTHETICAL PROTEIN
E: HYPOTHETICAL PROTEIN
F: HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)85,7416
Polymers85,7416
Non-polymers00
Water00
1
A: HYPOTHETICAL PROTEIN
C: HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYPOTHETICAL PROTEIN
E: HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
D: HYPOTHETICAL PROTEIN
F: HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,5802
Polymers28,5802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.682, 108.999, 70.088
Angle α, β, γ (deg.)90.00, 110.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HYPOTHETICAL PROTEIN / VACV-DUKE-037 / VIROKINE / VACV026 / N1L


Mass: 14290.240 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q49PX0
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 40 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN E, CYS 40 TO SER ENGINEERED RESIDUE IN CHAIN F, CYS 40 TO SER
Has protein modificationY
Sequence detailsCYS 40 WAS MUTATED TO SER SEMET WAS INCORPORATED IN PLACE OF MET FO R PHASING

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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: 3.2 Å3/Da / Density % sol: 61.21 %
Crystal growpH: 6.2
Details: 0.2 M NA/K PHOSPHATE, 0.2 M NACL AND 10% PEG 8000, PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 22319 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 11.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→30 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NCS CONSTRAINTS USED THROUGHOUT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 1094 4.9 %RANDOM
Rwork0.2372 ---
obs0.2372 22413 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 75 Å2
Baniso -1Baniso -2Baniso -3
1--11.359 Å20 Å2-21.454 Å2
2--12.159 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 0 0 5730
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.45
X-RAY DIFFRACTIONc_mcangle_it7.68
X-RAY DIFFRACTIONc_scbond_it11.27
X-RAY DIFFRACTIONc_scangle_it15.410
Refine LS restraints NCSNCS model details: CONSTRAINTS
LS refinement shellResolution: 2.9→2.95 Å / Total num. of bins used: 21
RfactorNum. reflection% reflection
Rfree0.436 56 4.9 %
Rwork0.5279 1000 -
obs--100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM

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