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- PDB-8izu: Crystal structure of the N-terminal domain (residues 1-137) of MPXV A7 -

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Basic information

Entry
Database: PDB / ID: 8izu
TitleCrystal structure of the N-terminal domain (residues 1-137) of MPXV A7
ComponentsVirion morphogenesis protein OPG132
KeywordsVIRAL PROTEIN / MPXV / A7 / N-terminus
Function / homologyPoxvirus A6 / Poxvirus A6 protein / virion component / host cell cytoplasm / NICKEL (II) ION / Virion morphogenesis protein OPG132
Function and homology information
Biological speciesMonkeypox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsNi, X.C. / Lei, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0702004 China
CitationJournal: Virol Sin / Year: 2024
Title: Structural analysis of conformational changes in the mpox virus A7 protein.
Authors: Ni, X. / Wang, K. / Han, Y. / Lei, J.
History
DepositionApr 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Virion morphogenesis protein OPG132
B: Virion morphogenesis protein OPG132
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4664
Polymers32,3152
Non-polymers1512
Water1,56787
1
A: Virion morphogenesis protein OPG132
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3083
Polymers16,1581
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Virion morphogenesis protein OPG132


Theoretical massNumber of molelcules
Total (without water)16,1581
Polymers16,1581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.903, 140.327, 153.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Virion morphogenesis protein OPG132


Mass: 16157.606 Da / Num. of mol.: 2 / Fragment: N-terminal domain(residues 1-137)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monkeypox virus / Gene: OPG132, MPXVgp117 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DNA4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.54→19.45 Å / Num. obs: 14013 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.997 / Net I/σ(I): 14.1
Reflection shellResolution: 2.54→2.65 Å / Num. unique obs: 1676 / CC1/2: 0.954

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IZT

8izt


Resolution: 2.54→19.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.157 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.399 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23776 677 4.9 %RANDOM
Rwork0.20106 ---
obs0.20288 13250 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.853 Å2
Baniso -1Baniso -2Baniso -3
1-8.66 Å20 Å2-0 Å2
2---1.36 Å20 Å2
3----7.3 Å2
Refinement stepCycle: 1 / Resolution: 2.54→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2206 0 7 87 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172164
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6393066
X-RAY DIFFRACTIONr_angle_other_deg1.3091.5855031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81623.684114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99815444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8681511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.9297.1491098
X-RAY DIFFRACTIONr_mcbond_other6.897.1481097
X-RAY DIFFRACTIONr_mcangle_it9.90110.7091371
X-RAY DIFFRACTIONr_mcangle_other9.90710.7131372
X-RAY DIFFRACTIONr_scbond_it6.9087.6851172
X-RAY DIFFRACTIONr_scbond_other6.8567.6861172
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.57711.2611692
X-RAY DIFFRACTIONr_long_range_B_refined13.10582.3372589
X-RAY DIFFRACTIONr_long_range_B_other13.10882.3622579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4276 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 52 -
Rwork0.351 959 -
obs--100 %

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