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- PDB-2wux: the crystal structure of recombinant baculovirus polyhedra -

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Basic information

Entry
Database: PDB / ID: 2wux
Titlethe crystal structure of recombinant baculovirus polyhedra
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / MICROCRYSTALS / POLYHEDRA / VIRAL OCCLUSION BODY / VIRAL CAPSID
Function / homologyPolyhedrin / Polyhedrin / viral occlusion body / host cell nuclear matrix / structural molecule activity / identical protein binding / Polyhedrin
Function and homology information
Biological speciesAUTOGRAPHA CALIFORNICA NUCLEAR POLYHEDROSIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.838 Å
AuthorsJi, X. / Sutton, G. / Evans, G. / Axford, D. / Owen, R. / Stuart, D.I.
CitationJournal: Embo J. / Year: 2010
Title: How Baculovirus Polyhedra Fit Square Pegs Into Round Holes to Robustly Package Viruses.
Authors: Ji, X. / Sutton, G. / Evans, G. / Axford, D. / Owen, R. / Stuart, D.I.
History
DepositionOct 10, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLYHEDRIN


Theoretical massNumber of molelcules
Total (without water)28,7371
Polymers28,7371
Non-polymers00
Water1,58588
1
A: POLYHEDRIN
x 12


Theoretical massNumber of molelcules
Total (without water)344,84112
Polymers344,84112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation6_566z,-x+1,-y+11
Buried area41420 Å2
ΔGint-189.2 kcal/mol
Surface area122590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.582, 102.582, 102.582
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 POLYHEDRIN


Mass: 28736.764 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AUTOGRAPHA CALIFORNICA NUCLEAR POLYHEDROSIS VIRUS
Plasmid: PBACPAK9 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P04871
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 25 TO ASP
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

CrystalDensity Matthews: 1.57 Å3/Da / Density % sol: 21.5 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778, 0.9778
DetectorType: RAYONIX / Detector: CCD / Date: Mar 12, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 15809 / % possible obs: 100 % / Observed criterion σ(I): -1.5 / Redundancy: 14.7 % / Biso Wilson estimate: 22.75 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 12.1
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.838→36.268 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.57 / Stereochemistry target values: ML / Details: RESIDUES 3-7 WERE TRACED AS POLY ALA MODEL
RfactorNum. reflection% reflection
Rfree0.217 787 5 %
Rwork0.1637 --
obs0.1663 15762 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.351 Å2 / ksol: 0.445 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Refinement stepCycle: LAST / Resolution: 1.838→36.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 88 1840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071801
X-RAY DIFFRACTIONf_angle_d1.0422446
X-RAY DIFFRACTIONf_dihedral_angle_d17.99654
X-RAY DIFFRACTIONf_chiral_restr0.074262
X-RAY DIFFRACTIONf_plane_restr0.005315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8383-1.95340.29741380.26512451X-RAY DIFFRACTION100
1.9534-2.10430.27291410.1932471X-RAY DIFFRACTION99
2.1043-2.3160.22411150.16762485X-RAY DIFFRACTION100
2.316-2.6510.23481330.15582465X-RAY DIFFRACTION100
2.651-3.33970.19741220.14262528X-RAY DIFFRACTION100
3.3397-36.27530.1841380.15032575X-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)
10.8070.0060.40010.8333-0.15760.2208-0.3128-0.8419-0.21770.2691-0.00020.22950.15310.06740.01540.36480.0139-0.00940.4573-0.0120.290175.77435.826141.4655
20.45080.0318-0.08160.20330.23260.44670.0208-0.0275-0.0160.02130.00360.0390.0230.0677-0.03020.10350.00150.00950.11180.00060.149675.044940.413112.107
30.11580.12440.02180.20910.21080.4013-0.0686-0.0588-0.02780.00580.0114-0.04270.0080.15410.06540.17710.0185-0.00260.17470.00030.211665.671132.59979.4605
40.7190.39450.41940.2390.00820.13130.06270.0586-0.15660.01090.0125-0.06620.04050.0695-0.05690.14830.0115-0.00630.1876-0.02390.203583.97638.368112.3876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:51)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 52:141)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 142:168)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 169:245)

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