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- PDB-7qrr: Crystal structure of Noumeavirus NMV_189 protein -

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Basic information

Entry
Database: PDB / ID: 7qrr
TitleCrystal structure of Noumeavirus NMV_189 protein
ComponentsNMV_189 protein
KeywordsVIRAL PROTEIN / Receptor Binding Protein / Fiber head
Function / homologyPHOSPHATE ION / Secreted protein
Function and homology information
Biological speciesNoumeavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: NMV_189 protein
A: NMV_189 protein
B: NMV_189 protein
C: NMV_189 protein
D: NMV_189 protein
E: NMV_189 protein
G: NMV_189 protein
H: NMV_189 protein
I: NMV_189 protein
J: NMV_189 protein
K: NMV_189 protein
L: NMV_189 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,27914
Polymers191,14812
Non-polymers1302
Water35,5081971
1
F: NMV_189 protein
A: NMV_189 protein
G: NMV_189 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8234
Polymers47,7873
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-39 kcal/mol
Surface area17300 Å2
MethodPISA
2
B: NMV_189 protein
C: NMV_189 protein
E: NMV_189 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8824
Polymers47,7873
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-36 kcal/mol
Surface area17250 Å2
MethodPISA
3
D: NMV_189 protein
K: NMV_189 protein
L: NMV_189 protein


Theoretical massNumber of molelcules
Total (without water)47,7873
Polymers47,7873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-31 kcal/mol
Surface area17100 Å2
MethodPISA
4
H: NMV_189 protein
J: NMV_189 protein

I: NMV_189 protein


Theoretical massNumber of molelcules
Total (without water)47,7873
Polymers47,7873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_343-x-3/2,y-1/2,-z-21
Buried area5520 Å2
ΔGint-32 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.567, 111.852, 127.897
Angle α, β, γ (deg.)90.000, 122.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-355-

HOH

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Components

#1: Protein
NMV_189 protein


Mass: 15929.025 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Noumeavirus / Gene: NMV_189 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: A0A1Q1PNC6
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1971 / 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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 4000 (w/v), 10% MPD (v/v), 0.1M AmSO4, 0.1M NaCl, 0.1M NaCaco

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→46.66 Å / Num. obs: 202894 / % possible obs: 98.4 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.029 / Rrim(I) all: 0.082 / Net I/σ(I): 16.7 / Num. measured all: 1558992 / Scaling rejects: 23
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
1.9-1.9380.3987906099230.9430.150.4264.897.2
10.41-46.667.50.05967012900.9980.0190.05431.697.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
SHELXphasing
PHENIX1.8.4refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.79 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 10162 5.01 %random
Rwork0.1617 ---
obs0.1632 202869 98.28 %-
Displacement parametersBiso max: 64.02 Å2 / Biso mean: 23.9957 Å2 / Biso min: 11.55 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12970 0 6 1971 14947

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