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- PDB-5mnd: SFX structure of Cydia pomonella granulovirus using a double flow... -

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Basic information

Entry
Database: PDB / ID: 5mnd
TitleSFX structure of Cydia pomonella granulovirus using a double flow-focusing nozzle
ComponentsGranulin
KeywordsVIRAL PROTEIN / SFX / granulovirus / in vivo crystals / nanocrystals
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Granulin
Function and homology information
Biological speciesCydia pomonella granulosis virus
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsOberthuer, D. / Chapman, H. / Doerner, K. / Xavier, P.L.
Funding support Germany, United States, 4items
OrganizationGrant numberCountry
BMBF05E13GU1 Germany
BMBF05K13GUK Germany
BMBF05K2012 Germany
National Science Foundation (NSF, United States)1231306). United States
CitationJournal: Sci Rep / Year: 2017
Title: Double-flow focused liquid injector for efficient serial femtosecond crystallography.
Authors: Oberthuer, D. / Knoska, J. / Wiedorn, M.O. / Beyerlein, K.R. / Bushnell, D.A. / Kovaleva, E.G. / Heymann, M. / Gumprecht, L. / Kirian, R.A. / Barty, A. / Mariani, V. / Tolstikova, A. / ...Authors: Oberthuer, D. / Knoska, J. / Wiedorn, M.O. / Beyerlein, K.R. / Bushnell, D.A. / Kovaleva, E.G. / Heymann, M. / Gumprecht, L. / Kirian, R.A. / Barty, A. / Mariani, V. / Tolstikova, A. / Adriano, L. / Awel, S. / Barthelmess, M. / Dorner, K. / Xavier, P.L. / Yefanov, O. / James, D.R. / Nelson, G. / Wang, D. / Calvey, G. / Chen, Y. / Schmidt, A. / Szczepek, M. / Frielingsdorf, S. / Lenz, O. / Snell, E. / Robinson, P.J. / Sarler, B. / Belsak, G. / Macek, M. / Wilde, F. / Aquila, A. / Boutet, S. / Liang, M. / Hunter, M.S. / Scheerer, P. / Lipscomb, J.D. / Weierstall, U. / Kornberg, R.D. / Spence, J.C. / Pollack, L. / Chapman, H.N. / Bajt, S.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Mar 30, 2022Group: Advisory / Author supporting evidence / Database references
Category: database_2 / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Granulin


Theoretical massNumber of molelcules
Total (without water)28,7841
Polymers28,7841
Non-polymers00
Water1,44180
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_575-x,-y+2,z1
crystal symmetry operation3_559-x,y,-z+41
crystal symmetry operation4_579x,-y+2,-z+41
crystal symmetry operation5_366z-2,x+1,y+11
crystal symmetry operation6_368z-2,-x+1,-y+31
crystal symmetry operation7_766-z+2,-x+1,y+11
crystal symmetry operation8_768-z+2,x+1,-y+31
crystal symmetry operation9_447y-1,z-1,x+21
crystal symmetry operation10_647-y+1,z-1,-x+21
crystal symmetry operation11_487y-1,-z+3,-x+21
crystal symmetry operation12_687-y+1,-z+3,x+21
Buried area51470 Å2
ΔGint-339 kcal/mol
Surface area151650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.400, 103.400, 103.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-376-

HOH

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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 granulosis virus (isolate Mexico/1963)
References: UniProt: P87577
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 1.6 Å3/Da / Density % sol: 23.14 %
Crystal growTemperature: 293 K / Method: in cell
Details: We used Madex HP (Certisusa). Madex HP contains about 1E13 virus occlusion bodies (OB) per liter and the OBs were purified from the aqueous suspension by applying iterative washing and ...Details: We used Madex HP (Certisusa). Madex HP contains about 1E13 virus occlusion bodies (OB) per liter and the OBs were purified from the aqueous suspension by applying iterative washing and centrifugation cycles. The pellet was then re-suspended in ultra-pure water at pH7. After 3h of incubation at room temperature the supernatant, containing the almost pure OBs, was removed from the pellet and subjected to filtration steps through a sequence of stainless steel filters with decreasing pore sizes (20 um, 10 um, 5 um, 2 um, 0.5 m; all IDEX). To increase the concentration of CpGV to the desired 1E11 particles/ml for injection at LCLS, the suspension was subjected to centrifugation at 21,000 g, the supernatant was removed, and the pellet re-suspended. Size distribution and particle concentration was estimated using a Nanosight LM14 instrument (Malvern).

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.5498 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.55→32.7 Å / Num. obs: 6052 / % possible obs: 99.2 % / Redundancy: 1755.5 % / CC1/2: 0.99 / Net I/σ(I): 35.21
Reflection shellResolution: 2.56→2.651 Å / Redundancy: 351.9 % / Mean I/σ(I) obs: 8.57 / CC1/2: 0.965 / % possible all: 96.96

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G0Z

5g0z


Resolution: 2.56→32.7 Å / SU ML: 0.331465050494 / Cross valid method: FREE R-VALUE / σ(F): 1.385 / Phase error: 20.3617872178
RfactorNum. reflection% reflectionSelection details
Rfree0.207 601 9.93060145406 %Rfree from 5G0Z
Rwork0.154 ---
obs0.16 6052 99.2293818659 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.0136272722 Å2
Refinement stepCycle: LAST / Resolution: 2.56→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 0 80 2111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002706421870682102
X-RAY DIFFRACTIONf_angle_d0.5422547166552854
X-RAY DIFFRACTIONf_chiral_restr0.0449375355728299
X-RAY DIFFRACTIONf_plane_restr0.00292430002288372
X-RAY DIFFRACTIONf_dihedral_angle_d15.25070220061259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.820.3031420.2061329X-RAY DIFFRACTION97.1598414795
2.82-3.220.2211580.1641337X-RAY DIFFRACTION100
3.22-4.060.1811610.1391360X-RAY DIFFRACTION100
4.06-32.70.1821400.1411425X-RAY DIFFRACTION99.8086734694

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