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- PDB-5g3x: Structure of recombinant granulovirus polyhedrin -

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Basic information

Entry
Database: PDB / ID: 5g3x
TitleStructure of recombinant granulovirus polyhedrin
ComponentsGRANULOVIRUS POLYHEDRIN
KeywordsVIRAL PROTEIN / NATIVE CRYSTALS / NANO CRYSTALLOGRAPHY / IN VIVO CRYSTALLIZATION / VIRUS
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / structural molecule activity / Granulin
Function and homology information
Biological speciesCYDIA POMONELLA GRANULOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsBunker, R.D. / Chiu, E. / Metcalf, P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser.
Authors: Gati, C. / Oberthuer, D. / Yefanov, O. / Bunker, R.D. / Stellato, F. / Chiu, E. / Yeh, S.M. / Aquila, A. / Basu, S. / Bean, R. / Beyerlein, K.R. / Botha, S. / Boutet, S. / DePonte, D.P. / ...Authors: Gati, C. / Oberthuer, D. / Yefanov, O. / Bunker, R.D. / Stellato, F. / Chiu, E. / Yeh, S.M. / Aquila, A. / Basu, S. / Bean, R. / Beyerlein, K.R. / Botha, S. / Boutet, S. / DePonte, D.P. / Doak, R.B. / Fromme, R. / Galli, L. / Grotjohann, I. / James, D.R. / Kupitz, C. / Lomb, L. / Messerschmidt, M. / Nass, K. / Rendek, K. / Shoeman, R.L. / Wang, D. / Weierstall, U. / White, T.A. / Williams, G.J. / Zatsepin, N.A. / Fromme, P. / Spence, J.C. / Goldie, K.N. / Jehle, J.A. / Metcalf, P. / Barty, A. / Chapman, H.N.
History
DepositionMay 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Mar 15, 2017Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: GRANULOVIRUS POLYHEDRIN


Theoretical massNumber of molelcules
Total (without water)29,3791
Polymers29,3791
Non-polymers00
Water2,144119
1
A: GRANULOVIRUS POLYHEDRIN
x 12


Theoretical massNumber of molelcules
Total (without water)352,54312
Polymers352,54312
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area66560 Å2
ΔGint-350 kcal/mol
Surface area122870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.058, 102.058, 102.058
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 GRANULOVIRUS POLYHEDRIN


Mass: 29378.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CYDIA POMONELLA GRANULOVIRUS / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P87577
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 21

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Sample preparation

CrystalDensity Matthews: 1.47 Å3/Da / Density % sol: 16.6 % / Description: NONE
Crystal growpH: 7 / Details: IN VIVO CRYSTALLIZATION, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 5, 2009 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→27.28 Å / Num. obs: 21009 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 8.28 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 7.5
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JVB

3jvb


Resolution: 1.66→27.276 Å / SU ML: 0.18 / σ(F): 1.38 / Phase error: 17.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 2131 10.14 %
Rwork0.1492 --
obs0.1535 21009 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.04 Å2
Refinement stepCycle: LAST / Resolution: 1.66→27.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 0 119 1990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071987
X-RAY DIFFRACTIONf_angle_d0.8622711
X-RAY DIFFRACTIONf_dihedral_angle_d15.9921195
X-RAY DIFFRACTIONf_chiral_restr0.052286
X-RAY DIFFRACTIONf_plane_restr0.006357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6604-1.6990.30541620.25431223X-RAY DIFFRACTION100
1.699-1.74150.23981440.221217X-RAY DIFFRACTION100
1.7415-1.78860.25141480.20851246X-RAY DIFFRACTION100
1.7886-1.84120.2811380.18851279X-RAY DIFFRACTION100
1.8412-1.90060.22261450.17821228X-RAY DIFFRACTION100
1.9006-1.96850.18691600.16131246X-RAY DIFFRACTION100
1.9685-2.04730.19341240.13791242X-RAY DIFFRACTION100
2.0473-2.14050.15141550.1251258X-RAY DIFFRACTION100
2.1405-2.25330.18621150.13031275X-RAY DIFFRACTION100
2.2533-2.39440.17351380.11691243X-RAY DIFFRACTION100
2.3944-2.57910.16671390.13261280X-RAY DIFFRACTION100
2.5791-2.83840.1891360.12961260X-RAY DIFFRACTION100
2.8384-3.24850.15681380.12161261X-RAY DIFFRACTION100
3.2485-4.09060.16481540.12311278X-RAY DIFFRACTION100
4.0906-27.27970.19471350.16381342X-RAY DIFFRACTION100

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