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- PDB-7qrj: Crystal structure of Zamilon vitis protein Zav_19 -

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Basic information

Entry
Database: PDB / ID: 7qrj
TitleCrystal structure of Zamilon vitis protein Zav_19
ComponentsZav_19 protein
KeywordsVIRAL PROTEIN / Receptor Binding Protein Fiber head
Function / homologyMinor virion protein
Function and homology information
Biological speciesZamilon virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å
AuthorsJeudy, S. / Abergel, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0001 France
CitationJournal: To Be Published
Title: The fibre head structure used by unrelated families of viruses is unexpectedly a major component of the Marseilleviridae and Zamilon virophages capsids
Authors: Jeudy, S. / Abergel, C.
History
DepositionJan 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zav_19 protein
B: Zav_19 protein
C: Zav_19 protein
D: Zav_19 protein
E: Zav_19 protein
F: Zav_19 protein


Theoretical massNumber of molelcules
Total (without water)117,6116
Polymers117,6116
Non-polymers00
Water25,9061438
1
A: Zav_19 protein
B: Zav_19 protein
E: Zav_19 protein


Theoretical massNumber of molelcules
Total (without water)58,8063
Polymers58,8063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-78 kcal/mol
Surface area19700 Å2
MethodPISA
2
C: Zav_19 protein
D: Zav_19 protein
F: Zav_19 protein


Theoretical massNumber of molelcules
Total (without water)58,8063
Polymers58,8063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-77 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.367, 103.258, 102.299
Angle α, β, γ (deg.)90.000, 131.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Zav_19 protein


Mass: 19601.871 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zamilon virus / Gene: za3_19 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: A0A2P1EHJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1438 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 3350, ammonium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.38→45.25 Å / Num. obs: 245617 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.029 / Rrim(I) all: 0.064 / Net I/σ(I): 13.7 / Num. measured all: 1177549 / Scaling rejects: 40662
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.38-1.43.90.2247557121120.9370.1270.2554.199.4
7.56-45.254.70.059735015640.9660.0320.06725.799.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
Aimless0.7.1data scaling
SHELXphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.38→45.25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.165 12263 5 %random selection
Rwork0.141 ---
obs0.142 245479 99.84 %-
Displacement parametersBiso max: 56.08 Å2 / Biso mean: 16.019 Å2 / Biso min: 5.97 Å2
Refinement stepCycle: LAST / Resolution: 1.38→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8190 0 0 1438 9628
LS refinement shellResolution: 1.38→1.4 Å
RfactorNum. reflection% reflection
Rfree0.2603 442 5.7 %
Rwork0.2052 7691 -
obs--0.99 %

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