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- PDB-4izk: Crystal structure of yellowtail ascites virus VP4 protease active... -

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Basic information

Entry
Database: PDB / ID: 4izk
TitleCrystal structure of yellowtail ascites virus VP4 protease active site mutant (K674A) reveals both an acyl-enzyme complex and an empty active site
Components(Yellowtail Ascites Virus (YAV) VP4 protease) x 2
KeywordsHYDROLASE / VIRAL PROTEASE / BIRNAVIRUS / SERINE-LYSINE DYAD MECHANISM / ALPHA-BETA PROTEIN FOLD / LYSINE GENERAL BASE / ACYL-ENZYME / PRODUCT COMPLEX
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 / cytoplasm
Similarity search - Function
Ribosomal Protein S5; domain 2 - #110 / 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. ...Ribosomal Protein S5; domain 2 - #110 / 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. / Ribosomal Protein S5; domain 2 / Viral coat protein subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Structural polyprotein
Similarity search - Component
Biological speciesYellowtail ascites virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPaetzel, M. / Chung, I.Y.W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structures of Yellowtail Ascites Virus VP4 Protease: TRAPPING AN INTERNAL CLEAVAGE SITE TRANS ACYL-ENZYME COMPLEX IN A NATIVE SER/LYS DYAD ACTIVE SITE.
Authors: Chung, I.Y. / Paetzel, M.
History
DepositionJan 30, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 27, 2013ID: 4HHC
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Yellowtail Ascites Virus (YAV) VP4 protease
B: Yellowtail Ascites Virus (YAV) VP4 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6495
Polymers44,5232
Non-polymers1273
Water5,765320
1
A: Yellowtail Ascites Virus (YAV) VP4 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2942
Polymers22,2691
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Yellowtail Ascites Virus (YAV) VP4 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3563
Polymers22,2531
Non-polymers1022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.520, 273.520, 273.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-930-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Yellowtail Ascites Virus (YAV) VP4 protease


Mass: 22269.332 Da / Num. of mol.: 1 / Mutation: K674A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellowtail ascites virus / Strain: Y-6 / Gene: VIRAL PROTEIN 4 (VP4) / Plasmid: PET28B+ / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: P89521, EC: 3.4.21.115
#2: Protein Yellowtail Ascites Virus (YAV) VP4 protease


Mass: 22253.332 Da / Num. of mol.: 1 / Mutation: K674A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yellowtail ascites virus / Strain: Y-6 / Gene: VIRAL PROTEIN 4 (VP4) / Plasmid: PET28B+ / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) / References: UniProt: P89521, EC: 3.4.21.115
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 2000, 0.1 M MES, 0.45 M MAGNESIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2010
Details: DCM WITH CRYO-COOLED. 1ST CRYSTAL SAGITTALLY BENT. 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR.
RadiationMonochromator: A DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→55.8 Å / Num. all: 39388 / Num. obs: 39388 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 6.5 / Num. unique all: 5637 / % possible all: 100

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IZJ

4izj


Resolution: 2.3→55.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.45 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19685 1978 5 %RANDOM
Rwork0.17269 ---
obs0.17394 39388 100 %-
all-39388 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.166 Å2
Refinement stepCycle: LAST / Resolution: 2.3→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 6 320 3352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193083
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.994212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97326.393122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73615485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.075157
X-RAY DIFFRACTIONr_chiral_restr0.1210.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0222347
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 123 -
Rwork0.21 2474 -
obs-5637 100 %

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