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- PDB-8xy4: Crystal structure of VACV N1 protein -

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Basic information

Entry
Database: PDB / ID: 8xy4
TitleCrystal structure of VACV N1 protein
ComponentsN1L
KeywordsVIRAL PROTEIN / VACV / N1
Function / homologyOrthopoxvirus, Protein N1 / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / symbiont-mediated perturbation of host apoptosis / Uncharacterized protein
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsNi, X.C. / Lei, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0702004 China
CitationJournal: To Be Published
Title: Crystal structure of VACV N1 protein
Authors: Ni, X.C. / Lei, J.
History
DepositionJan 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N1L


Theoretical massNumber of molelcules
Total (without water)16,1491
Polymers16,1491
Non-polymers00
Water1,53185
1
A: N1L

A: N1L


Theoretical massNumber of molelcules
Total (without water)32,2992
Polymers32,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area2410 Å2
ΔGint-3 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.860, 77.860, 111.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-280-

HOH

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Components

#1: Protein N1L / N1L protein


Mass: 16149.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus
Gene: VACV_BRZ_SERRO2_026, N1L, 44/47.1_rMVA_020, List025, m8028L, mO028L
Production host: Escherichia coli (E. coli) / References: UniProt: Q49PX0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.42→42.94 Å / Num. obs: 8116 / % possible obs: 99.9 % / Redundancy: 35.7 % / CC1/2: 0.999 / Net I/σ(I): 24.5
Reflection shellResolution: 2.42→2.51 Å / Num. unique obs: 826 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→42.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.324 / SU ML: 0.141 / Cross valid method: FREE R-VALUE / ESU R: 0.248 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2062 405 5.005 %
Rwork0.1701 7687 -
all0.172 --
obs-8092 99.84 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.187 Å2
Baniso -1Baniso -2Baniso -3
1-0.969 Å20.484 Å2-0 Å2
2--0.969 Å2-0 Å2
3----3.143 Å2
Refinement stepCycle: LAST / Resolution: 2.42→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 85 1099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131055
X-RAY DIFFRACTIONr_bond_other_d0.0010.017977
X-RAY DIFFRACTIONr_angle_refined_deg1.661.6421429
X-RAY DIFFRACTIONr_angle_other_deg1.4121.5892264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4665129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9822.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6515201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4521510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02234
X-RAY DIFFRACTIONr_nbd_refined0.2110.2232
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.2896
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2505
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.272
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.24
X-RAY DIFFRACTIONr_nbd_other0.2020.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.28
X-RAY DIFFRACTIONr_mcbond_it3.7764.352495
X-RAY DIFFRACTIONr_mcbond_other3.7634.346494
X-RAY DIFFRACTIONr_mcangle_it5.1626.517619
X-RAY DIFFRACTIONr_mcangle_other5.1646.525620
X-RAY DIFFRACTIONr_scbond_it4.814.782560
X-RAY DIFFRACTIONr_scbond_other4.7784.77558
X-RAY DIFFRACTIONr_scangle_it6.6156.973806
X-RAY DIFFRACTIONr_scangle_other6.6136.975806
X-RAY DIFFRACTIONr_lrange_it8.43650.2541242
X-RAY DIFFRACTIONr_lrange_other8.44250.1791235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.4830.328340.246536X-RAY DIFFRACTION99.1304
2.483-2.5510.281310.24531X-RAY DIFFRACTION99.6454
2.551-2.6250.33280.22525X-RAY DIFFRACTION100
2.625-2.7050.25200.187514X-RAY DIFFRACTION99.8131
2.705-2.7940.207250.174495X-RAY DIFFRACTION100
2.794-2.8920.163190.151490X-RAY DIFFRACTION100
2.892-3.0010.253210.166464X-RAY DIFFRACTION100
3.001-3.1230.246220.171452X-RAY DIFFRACTION99.7895
3.123-3.2610.201190.177431X-RAY DIFFRACTION100
3.261-3.420.242230.173412X-RAY DIFFRACTION100
3.42-3.6050.17210.18399X-RAY DIFFRACTION100
3.605-3.8230.25240.18368X-RAY DIFFRACTION99.7455
3.823-4.0860.227160.137368X-RAY DIFFRACTION100
4.086-4.4120.2190.134328X-RAY DIFFRACTION100
4.412-4.8310.135150.139320X-RAY DIFFRACTION100
4.831-5.3970.17260.138271X-RAY DIFFRACTION100
5.397-6.2260.265100.181263X-RAY DIFFRACTION100
6.226-7.6090.159140.169223X-RAY DIFFRACTION100
7.609-10.6930.128100.132179X-RAY DIFFRACTION100
10.693-42.940.24980.274118X-RAY DIFFRACTION98.4375

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