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- PDB-9gnp: SFX structure of Cydia pomonella granulovirus using aerosol sampl... -

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Basic information

Entry
Database: PDB / ID: 9gnp
TitleSFX structure of Cydia pomonella granulovirus using aerosol sample injection
ComponentsGranulin
KeywordsVIRAL PROTEIN / Granulovirus / SFX / Electrospray injection
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Granulin
Function and homology information
Biological speciesCydia pomonella granulovirus
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKoua, F.H. / Kim, Y. / Kim, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SFX structure of Cydia pomonella granulovirus using aerosol sample injection
Authors: Koua, F.H.
History
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 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: Granulin


Theoretical massNumber of molelcules
Total (without water)28,7841
Polymers28,7841
Non-polymers00
Water18010
1
A: Granulin
x 12


Theoretical massNumber of molelcules
Total (without water)345,40612
Polymers345,40612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area78730 Å2
ΔGint-365 kcal/mol
Surface area115970 Å2
Unit cell
Length a, b, c (Å)100.130, 100.130, 100.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Granulin / Matrix protein


Mass: 28783.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cydia pomonella granulovirus / References: UniProt: X4ZEF4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.43 Å3/Da / Density % sol: 14.28 %
Crystal growTemperature: 293 K / Method: in cell / Details: In vivo

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 2.033 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Mar 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.033 Å / Relative weight: 1
ReflectionResolution: 2.3→40.88 Å / Num. obs: 6978 / % possible obs: 92 % / Redundancy: 761 % / Biso Wilson estimate: 54.26 Å2 / CC1/2: 0.9842 / CC star: 0.996 / R split: 0.118 / Net I/σ(I): 6.22
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 26 % / Mean I/σ(I) obs: 0.22 / Num. unique obs: 1053 / CC1/2: 0.1214 / CC star: 0.4699 / R split: 3.85 / % possible all: 69
Serial crystallography measurementFocal spot size: 3 µm2 / Pulse duration: 25 fsec. / Pulse energy: 2850 µJ / Pulse photon energy: 6.1 keV
Serial crystallography sample deliveryDescription: Electrospray / Method: injection

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Processing

Software
NameVersionClassification
PHENIX(1.21.1-5286_9999: ???)refinement
CrystFELdata scaling
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→40.88 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 34.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 689 9.87 %
Rwork0.1784 --
obs0.1845 6978 92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 0 10 2033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052089
X-RAY DIFFRACTIONf_angle_d0.7972840
X-RAY DIFFRACTIONf_dihedral_angle_d15.136779
X-RAY DIFFRACTIONf_chiral_restr0.048299
X-RAY DIFFRACTIONf_plane_restr0.008371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.42341020.3372951X-RAY DIFFRACTION69
2.48-2.730.35671290.27291227X-RAY DIFFRACTION91
2.73-3.120.2841480.2071332X-RAY DIFFRACTION99
3.12-3.930.21571530.16551366X-RAY DIFFRACTION100
3.93-40.880.20361570.15111413X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19150.0404-0.1170.0649-0.05410.041-0.01770.111-0.2198-0.2211-0.22210.38620.18860.183500.51010.0927-0.02230.4643-0.09610.588821.99648.71287.3249
20.28580.1414-0.22150.13210.07510.3287-0.04770.01270.0438-0.04980.0329-0.0014-0.00690.05200.3745-0.0091-0.00150.39850.01060.380220.604-12.8835-36.2334
30.012-0.01060.0151-0.00670.0270.0026-0.096-0.0074-0.0803-0.00120.0835-0.35320.50570.2033-00.59910.04120.09270.5759-0.00810.688532.1258-18.4437-34.3852
40.0415-0.0709-0.12960.0157-0.18870.00980.09090.08720.00670.0011-0.05680.0286-0.03860.017100.36510.0258-0.02280.41760.0010.413332.7121-13.2039-39.2991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 168 )
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 188 )
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 248 )

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