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- PDB-2pnl: Crystal structure of VP4 protease from infectious pancreatic necr... -

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Basic information

Entry
Database: PDB / ID: 2pnl
TitleCrystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1
ComponentsProtease VP4
KeywordsHYDROLASE / acyl-enzyme / protease / Ser/Lys dyad / viral protease / substrate complex / 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
GUANIDINE / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesInfectious pancreatic necrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPaetzel, M. / Lee, J. / Feldman, A.R. / Delmas, B.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction.
Authors: Lee, J. / Feldman, A.R. / Delmas, B. / Paetzel, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification, crystallization and preliminary X-ray analysis of truncated and mutant forms of VP4 protease from infectious pancreatic necrosis virus.
Authors: Lee, J. / Feldman, A.R. / Chiu, E. / Chan, C. / Kim, Y.-N. / Delmas, B. / Paetzel, M.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease VP4
B: Protease VP4
C: Protease VP4
D: Protease VP4
E: Protease VP4
F: Protease VP4
G: Protease VP4
H: Protease VP4
I: Protease VP4
J: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,56627
Polymers217,56210
Non-polymers1,00417
Water21,9061216
1
A: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8743
Polymers21,7561
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9334
Polymers21,7561
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9334
Polymers21,7561
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8152
Polymers21,7561
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8743
Polymers21,7561
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8152
Polymers21,7561
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Protease VP4


Theoretical massNumber of molelcules
Total (without water)21,7561
Polymers21,7561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9334
Polymers21,7561
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8152
Polymers21,7561
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Protease VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8152
Polymers21,7561
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.703, 69.262, 191.388
Angle α, β, γ (deg.)93.06, 95.03, 97.56
Int Tables number1
Space group name H-MP1
Detailsthe enzyme is a monomer in solution during purification, but forms an intermolecular acyl-enzyme complex with this construct, such that 6 of the 10 molecules in the asymmetric unit are linked via the nucleophile Ser633 and the C-terminal Ala716 (P1 residue of the VP4 internal cleavge site).

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Components

#1: Protein
Protease VP4


Mass: 21756.182 Da / Num. of mol.: 10 / Fragment: VP4tri (residues 514-716) / Mutation: K674A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious pancreatic necrosis virus / Genus: Aquabirnavirus / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q703G9, UniProt: A1XQQ8*PLUS
#2: Chemical
ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CH5N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1216 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 35% PEG 4000, 0.4M LiSO4, 0.4M Guanidine-HCl , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.21→182.57 Å / Num. all: 103935 / Num. obs: 103935 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.7
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.5 / Num. unique all: 9718 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→182.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.883 / SU B: 6.397 / SU ML: 0.167 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5185 5 %RANDOM
Rwork0.19 ---
all0.2 103935 --
obs0.194 103863 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.86 Å2-0.65 Å2
2--1.66 Å2-0.26 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.21→182.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15142 0 68 1216 16426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215481
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9921086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9252002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.47426.074647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.978152453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6431557
X-RAY DIFFRACTIONr_chiral_restr0.120.22450
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211833
X-RAY DIFFRACTIONr_nbd_refined0.2380.27248
X-RAY DIFFRACTIONr_nbtor_refined0.3060.210423
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.21235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.2167
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.243
X-RAY DIFFRACTIONr_mcbond_it1.0831.510438
X-RAY DIFFRACTIONr_mcangle_it1.591216235
X-RAY DIFFRACTIONr_scbond_it2.67535643
X-RAY DIFFRACTIONr_scangle_it3.9684.54851
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 367 -
Rwork0.201 7033 -
obs-7400 95.67 %

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