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- PDB-2z7j: Structural insights into de multifunctional VP3 protein of birnav... -

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Basic information

Entry
Database: PDB / ID: 2z7j
TitleStructural insights into de multifunctional VP3 protein of birnaviruses:gold derivative
ComponentsCapsid assembly protein VP3
KeywordsVIRAL PROTEIN / helix / Capsid protein / Hydrolase / Protease / Serine protease / Virion
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding
Similarity search - Function
Capsid protein VP3, domain 1 / Birnavirus VP3 protein, domain 2 / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein ...Capsid protein VP3, domain 1 / Birnavirus VP3 protein, domain 2 / Birnavirus VP3, domain 2 / Birnavirus VP3, domain 1 / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protease domain / Birnavirus VP2 protein / Birnavirus VP3 protein / Birnavirus VP4 protein / Birnavirus VP4 protease domain profile. / Helicase, Ruva Protein; domain 3 / Viral coat protein subunit / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Structural polyprotein
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsCasanas, A. / Navarro, A. / Ferrer-Orta, C. / Gonzalez, D. / Rodriguez, J.F. / Verdaguer, N.
CitationJournal: Structure / Year: 2008
Title: Structural insights into the multifunctional protein VP3 of birnaviruses.
Authors: Casanas, A. / Navarro, A. / Ferrer-Orta, C. / Gonzalez, D. / Rodriguez, J.F. / Verdaguer, N.
History
DepositionAug 23, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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: Capsid assembly protein VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8814
Polymers14,2901
Non-polymers5913
Water52229
1
A: Capsid assembly protein VP3
hetero molecules

A: Capsid assembly protein VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7628
Polymers28,5802
Non-polymers1,1826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.749, 69.749, 71.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-3-

AU

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Components

#1: Protein Capsid assembly protein VP3


Mass: 14290.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Genus: Avibirnavirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25220
#2: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.5M NaCl 0.1M Sodium Acetate pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.039 1.040 1.037
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0391
21.041
31.0371
ReflectionResolution: 2.3→30 Å / Num. all: 7312 / Num. obs: 7312 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 2.3 Å / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
DNAdata collection
SHARPphasing
RefinementResolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.734 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28492 329 4.6 %RANDOM
Rwork0.23614 ---
obs0.23834 6832 97.93 %-
all-7161 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.341 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 3 29 1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221029
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.9621392
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32524.61552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.8915182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.871157
X-RAY DIFFRACTIONr_chiral_restr0.080.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02801
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2468
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.2712
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5831.5641
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04521009
X-RAY DIFFRACTIONr_scbond_it1.4653438
X-RAY DIFFRACTIONr_scangle_it2.4594.5383
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 18 -
Rwork0.246 414 -
obs--84.38 %
Refinement TLS params.Method: refined / Origin x: 23.1952 Å / Origin y: 10.4684 Å / Origin z: 33.3749 Å
111213212223313233
T-0.359 Å2-0.0172 Å20.0685 Å2--0.2711 Å2-0.0197 Å2---0.4635 Å2
L6.1383 °2-6.9535 °23.1038 °2-10.0572 °2-4.2964 °2--3.2496 °2
S0.2544 Å °0.5375 Å °0.1129 Å °-0.4032 Å °-0.4557 Å °-0.1956 Å °0.2365 Å °0.2315 Å °0.2013 Å °

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