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- PDB-2oh7: The Crystal Structure of Cypovirus Polyhedra containing the Human... -

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Basic information

Entry
Database: PDB / ID: 2oh7
TitleThe Crystal Structure of Cypovirus Polyhedra containing the Human ZIP-kinase
ComponentsPolyhedrin
KeywordsStructural Protein / RNA binding protein / beta sandwich / intracellular crystal / nucleotide binding
Function / homology
Function and homology information


GTP binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,9587
Polymers28,3601
Non-polymers1,5986
Water2,468137
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)359,49584
Polymers340,32412
Non-polymers19,17172
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation10_656-y+1,z,-x+11
Unit cell
Length a, b, c (Å)102.742, 102.742, 102.742
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-291-

HOH

21A-389-

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: 28360.355 Da / Num. of mol.: 1 / Mutation: N29S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Strain: CPV1 / Gene: Polyhedin / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 (IPLB-SF21AE) / References: UniProt: O10693

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Non-polymers , 6 types, 143 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

Crystal growTemperature: 300 K
Details: The crystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell, temperature 300K

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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: 2.45→20 Å / Num. all: 6778 / Num. obs: 6770 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.025 / Net I/σ(I): 8.2
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.7 / Num. unique all: 656 / Χ2: 1.08 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OH6

2oh6


Resolution: 2.45→18.8 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.773 / SU ML: 0.2 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 644 9.6 %RANDOM
Rwork0.112 ---
all0.122 6744 --
obs0.122 6736 99.88 %-
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: 17.933 Å2
Refinement stepCycle: LAST / Resolution: 2.45→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 95 137 2239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212157
X-RAY DIFFRACTIONr_bond_other_d0.0010.021412
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9832946
X-RAY DIFFRACTIONr_angle_other_deg0.9443.0013397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3835246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48623.805113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97615327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0781514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined0.1920.2423
X-RAY DIFFRACTIONr_nbd_other0.1980.21423
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21010
X-RAY DIFFRACTIONr_nbtor_other0.0880.21091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2123
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.262
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.2200
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.246
X-RAY DIFFRACTIONr_mcbond_it0.7131.51590
X-RAY DIFFRACTIONr_mcbond_other0.1411.5500
X-RAY DIFFRACTIONr_mcangle_it0.94721982
X-RAY DIFFRACTIONr_scbond_it1.66731128
X-RAY DIFFRACTIONr_scangle_it2.4754.5964
LS refinement shellResolution: 2.45→2.517 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 52 -
Rwork0.15 432 -
obs-484 99.59 %

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