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- PDB-4izj: Crystal structure of yellowtail ascites virus VP4 protease with a... -

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Basic information

Entry
Database: PDB / ID: 4izj
TitleCrystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.
Components(Yellowtail Ascites Virus (YAV) VP4 ...) x 3
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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: 3R0B
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: 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_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 / _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_asym_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 1.4Dec 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,25913
Polymers111,6745
Non-polymers5858
Water4,882271
1
A: Yellowtail Ascites Virus (YAV) VP4 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4473
Polymers22,3441
Non-polymers1022
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)22,4853
Polymers22,3281
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Yellowtail Ascites Virus (YAV) VP4 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4072
Polymers22,3281
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Yellowtail Ascites Virus (YAV) VP4 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4993
Polymers22,3281
Non-polymers1702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Yellowtail Ascites Virus (YAV) VP4 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4232
Polymers22,3441
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.610, 64.330, 187.740
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Yellowtail Ascites Virus (YAV) VP4 ... , 3 types, 5 molecules AEBCD

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


Mass: 22344.418 Da / Num. of mol.: 2 / Mutation: N616D
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: 22328.418 Da / Num. of mol.: 2 / Mutation: N616D
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: Protein Yellowtail Ascites Virus (YAV) VP4 protease


Mass: 22328.418 Da / Num. of mol.: 1 / Mutation: N616D
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

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Non-polymers , 4 types, 279 molecules

#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35% PEG2000, 0.3M Magnesium Chloride, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 5, 2009 / Details: MULTILAYER OPTIC
RadiationMonochromator: VARIMAX CU HF OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→64.3 Å / Num. all: 33009 / Num. obs: 33009 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4043 / % possible all: 80.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PNM

2pnm


Resolution: 2.5→64.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.852 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24397 1669 5.1 %RANDOM
Rwork0.17828 ---
obs0.18167 33009 95.9 %-
all-33009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.761 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.32 Å2
2--0.02 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7596 0 31 271 7898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197769
X-RAY DIFFRACTIONr_angle_refined_deg0.91.99510588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45151009
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35626.343309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.19151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2231519
X-RAY DIFFRACTIONr_chiral_restr0.0350.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.0225881
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 88 -
Rwork0.251 1706 -
obs-4043 80.7 %

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