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- PDB-5a9p: Crystal structure of Operophtera brumata CPV18 polyhedra -

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Basic information

Entry
Database: PDB / ID: 5a9p
TitleCrystal structure of Operophtera brumata CPV18 polyhedra
ComponentsPOLYHEDRIN
KeywordsVIRAL PROTEIN / INSECT VIRUS OCCLUSION BODY / MICROCRYSTAL
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / GTP binding / ATP binding / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesOPEROPHTERA BRUMATA CYPOVIRUS 18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.476 Å
AuthorsJi, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Polyhedra Structures and the Evolution of the Insect Viruses.
Authors: Ji, X. / Axford, D. / Owen, R. / Evans, G. / Ginn, H.M. / Sutton, G. / Stuart, D.I.
History
DepositionJul 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)29,4373
Polymers28,4071
Non-polymers1,0302
Water4,558253
1
A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules

A: POLYHEDRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3119
Polymers85,2203
Non-polymers3,0916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area12710 Å2
ΔGint-68.8 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.770, 102.770, 102.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

21A-2029-

HOH

31A-2122-

HOH

41A-2181-

HOH

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Components

#1: Protein POLYHEDRIN /


Mass: 28406.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) OPEROPHTERA BRUMATA CYPOVIRUS 18 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q30C70
#2: 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
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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

CrystalDescription: 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: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.48→72.7 Å / Num. obs: 30415 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 12.9 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 7.1
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OH6

2oh6


Resolution: 1.476→72.669 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 13.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1475 1538 5.1 %
Rwork0.1302 --
obs0.1311 30415 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.476→72.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 63 253 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052124
X-RAY DIFFRACTIONf_angle_d1.1462901
X-RAY DIFFRACTIONf_dihedral_angle_d18.395777
X-RAY DIFFRACTIONf_chiral_restr0.067291
X-RAY DIFFRACTIONf_plane_restr0.005373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4763-1.5240.23881480.22822612X-RAY DIFFRACTION100
1.524-1.57840.21661300.20662588X-RAY DIFFRACTION100
1.5784-1.64160.23461220.18662612X-RAY DIFFRACTION100
1.6416-1.71630.19441230.16892634X-RAY DIFFRACTION100
1.7163-1.80680.18771430.15282590X-RAY DIFFRACTION100
1.8068-1.92010.17471360.14112617X-RAY DIFFRACTION100
1.9201-2.06830.13321510.11762611X-RAY DIFFRACTION100
2.0683-2.27650.12871460.10652608X-RAY DIFFRACTION100
2.2765-2.60590.12081370.10752635X-RAY DIFFRACTION100
2.6059-3.28320.12561510.1042647X-RAY DIFFRACTION100
3.2832-72.75750.11481510.10932723X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.1141 Å / Origin y: 21.1181 Å / Origin z: 8.7019 Å
111213212223313233
T0.0511 Å2-0.0009 Å20.0015 Å2-0.0477 Å2-0.0006 Å2--0.0497 Å2
L0.0019 °20.0003 °20.0025 °2-0.0027 °20.0018 °2--0.0037 °2
S-0.0007 Å °-0.0018 Å °-0.0001 Å °0.0002 Å °-0.0041 Å °-0.0018 Å °-0 Å °0.0017 Å °-0.0005 Å °
Refinement TLS groupSelection details: ALL

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