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- PDB-2oh5: The Crystal Structure of Infectious Cypovirus Polyhedra -

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Basic information

Entry
Database: PDB / ID: 2oh5
TitleThe Crystal Structure of Infectious Cypovirus Polyhedra
ComponentsPolyhedrin
KeywordsSTRUCTURAL PROTEIN / RNA BINDING PROTEIN / beta barrel / intracellular crystal / nucleotide binding
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / GTP binding / ATP binding / identical protein binding / ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesBombyx mori cypovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsCoulibaly, F. / Chiu, E. / Ikeda, K. / Gutmann, S. / Haebel, P.W. / Schulze-Briese, C. / Mori, H. / Metcalf, P.
CitationJournal: Nature / Year: 2007
Title: The molecular organization of cypovirus polyhedra.
Authors: Coulibaly, F. / Chiu, E. / Ikeda, K. / Gutmann, S. / Haebel, P.W. / Schulze-Briese, C. / Mori, H. / Metcalf, P.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9857
Polymers28,3871
Non-polymers1,5986
Water5,152286
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)359,82084
Polymers340,64912
Non-polymers19,17172
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
2
A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,97014
Polymers56,7752
Non-polymers3,19512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11430 Å2
ΔGint-102 kcal/mol
Surface area56880 Å2
MethodPISA
3
A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules

A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,95521
Polymers85,1623
Non-polymers4,79318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPQS
Unit cell
Length a, b, c (Å)102.777, 102.777, 102.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

21A-317-

HOH

31A-318-

HOH

41A-320-

HOH

51A-326-

HOH

61A-344-

HOH

71A-396-

HOH

DetailsThe whole micron-sized crystals, called polyhedra, are the biological units. Polyhedra crystallize in the cytoplasm of CPV-infected cells and protect the virus particles.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyhedrin / / C-polyhedrin


Mass: 28387.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The microcrystals of the polyhedrin protein, called polyhedra, are purified from CPV-infected silkworms, Bombyx Mori.
Source: (natural) Bombyx mori cypovirus 1 / Species: Cypovirus 1 / References: UniProt: O10693

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Non-polymers , 6 types, 292 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3

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Sample preparation

Crystal growTemperature: 298 K
Details: The microcrystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9983 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 5, 2006 / Details: MD2 diffractometer
RadiationMonochromator: sagitally horizontal focussing Si(111); meridionally vertical focussing Rh-coated mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9983 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. all: 12757 / Num. obs: 12630 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.9
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1242 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→18.76 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.968 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.154 1257 10 %RANDOM
Rwork0.093 ---
all0.099 12733 --
obs0.099 12605 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.483 Å2
Refinement stepCycle: LAST / Resolution: 1.98→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 95 286 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212213
X-RAY DIFFRACTIONr_bond_other_d0.0020.021473
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9823029
X-RAY DIFFRACTIONr_angle_other_deg0.8743.0013546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97323.559118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47915346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9471517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022460
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02474
X-RAY DIFFRACTIONr_nbd_refined0.2030.2466
X-RAY DIFFRACTIONr_nbd_other0.2010.21587
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21058
X-RAY DIFFRACTIONr_nbtor_other0.0850.21144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.276
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.2212
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.283
X-RAY DIFFRACTIONr_mcbond_it0.7641.51639
X-RAY DIFFRACTIONr_mcbond_other0.1741.5508
X-RAY DIFFRACTIONr_mcangle_it0.96822029
X-RAY DIFFRACTIONr_scbond_it1.84231167
X-RAY DIFFRACTIONr_scangle_it2.6854.5994
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 98 -
Rwork0.134 828 -
obs-926 100 %

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