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- PDB-2pnm: Crystal Structure of VP4 protease from infectious pancreatic necr... -

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Basic information

Entry
Database: PDB / ID: 2pnm
TitleCrystal Structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P6122
ComponentsProtease VP4
KeywordsHYDROLASE / protease / Ser/Lys dyad / viral protease
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
Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesInfectious pancreatic necrosis virus - Sp
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease VP4


Theoretical massNumber of molelcules
Total (without water)20,5941
Polymers20,5941
Non-polymers00
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.953, 76.953, 136.347
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsThis enzymes is a monomer in solution during purification.

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Components

#1: Protein Protease VP4


Mass: 20593.791 Da / Num. of mol.: 1 / Fragment: VP4hex (residues 524-716) / Mutation: K674A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious pancreatic necrosis virus - Sp
Genus: Aquabirnavirus / Species: Infectious pancreatic necrosis virus / Strain: serotype SP / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q703G9, UniProt: A1XQR0*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl pH 8.5, 22% PEG 2000 MME, 0.45M Calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→47.7 Å / Num. all: 11248 / Num. obs: 11248 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.5 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 23.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 9.8 / Num. unique all: 1584 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→25.52 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.271 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 538 4.8 %RANDOM
Rwork0.182 ---
all0.2 11248 --
obs0.184 11186 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.945 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 159 1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221367
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9831869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84827.36857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.175151
X-RAY DIFFRACTIONr_chiral_restr0.10.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021042
X-RAY DIFFRACTIONr_nbd_refined0.2140.2606
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2944
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.217
X-RAY DIFFRACTIONr_mcbond_it0.9241.5927
X-RAY DIFFRACTIONr_mcangle_it1.43421454
X-RAY DIFFRACTIONr_scbond_it2.0013490
X-RAY DIFFRACTIONr_scangle_it2.914.5415
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 44 -
Rwork0.17 750 -
obs-794 99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.4332-0.906819.16676.0134-13.790259.98020.4811.9647-0.06330.2684-2.5608-1.80740.78323.55422.07980.03350.0847-0.0650.14950.04950.211221.1153-10.925-4.3224
22.38961.77720.75752.8574-1.03522.44430.1001-0.01050.01160.15650.0027-0.02750.02010.0445-0.10280.05080.0037-0.0350.0215-0.00260.0496.3221-15.6809-9.9954
321.53561.566711.747110.50826.72970.81780.3417-1.4331.13321.1197-0.96140.0476-3.71581.17460.61970.4876-0.44970.00370.21790.0425-0.08211.1988-16.21327.9786
48.05950.978-3.3921.5605-0.18517.48040.2814-0.2098-0.3623-0.05630.0966-0.26220.37710.2344-0.3780.0806-0.0323-0.0750.0022-0.01840.03868.0194-20.9752-7.9427
57.90793.20076.502110.12866.464915.15350.09760.7854-0.1886-0.54690.5139-0.2051-0.15061.1165-0.61140.02330.009-0.04310.0166-0.0650.016316.233-16.0001-5.911
62.24082.87822.10894.05741.86143.97620.37130.0955-0.62610.33470.2165-0.40040.86310.5275-0.58780.13840.0878-0.1945-0.0539-0.06710.11915.4114-27.9351-2.6099
70.2742-0.24911.27266.8589-4.42387.51690.42050.2228-0.64340.20060.3691-0.3181.23480.1234-0.78960.25330.0739-0.2735-0.1646-0.09520.149611.0429-35.9201-6.4777
811.5063-2.84425.36310.9494-1.19272.50140.5030.7434-0.4375-0.5226-0.0522-0.61540.25250.3035-0.45080.06910.0027-0.04710.0218-0.01140.069310.2576-22.1995-8.4629
94.39322.13867.80813.5074-0.278820.6267-0.17890.10870.26840.01050.08760.3391-0.352-0.21190.0913-0.0120.0025-0.0213-0.02810.02090.06150.3128-10.962-13.2234
104.2008-0.07128.69350.17630.518320.52150.0901-0.1353-0.01520.10590.12420.0515-0.0443-0.3097-0.21430.014-0.0319-0.036-0.00470.00130.08268.7852-11.5491-2.9362
111.6482-0.18840.42852.84180.86711.25290.7128-0.5875-0.24820.5985-0.35950.07511.0652-0.2901-0.35330.2005-0.0807-0.169-0.05340.05740.00987.4994-25.27873.6909
123.63381.14981.19613.25452.80277.06250.19130.2187-0.76510.01020.0719-0.13530.822-0.0926-0.26320.1879-0.0532-0.1793-0.09020.02680.1092.9733-32.224-9.0907
1328.9802-8.1801-6.45859.30942.326615.2791-0.0211.3867-0.4489-0.3337-0.20440.15930.9058-0.33910.22540.1597-0.078-0.10930.07160.02980.0452-0.7621-24.1751-16.0097
142.2150.22310.87871.67081.91982.38320.5006-0.4407-0.47440.5837-0.12190.15650.8075-0.4158-0.37860.2342-0.1834-0.1283-0.01150.0802-0.0231-1.8673-30.176-2.5554
157.4756-7.2353-3.41313.6332.60769.61950.2075-0.7762-1.05560.81890.38940.06351.52630.0577-0.59680.3068-0.2748-0.2624-0.10290.16310.0433-1.9529-36.13881.2816
163.8597-5.85572.31313.5516-4.59681.63950.5263-0.6711-0.02711.0681-0.1090.6112-0.0408-0.8693-0.41730.0568-0.16060.04420.20440.0142-0.0619-6.986-18.43312.5434
1714.01946.69280.577810.4409-4.61873.330.0552-0.15560.55420.4880.01820.3365-0.1288-0.6572-0.07340.006-0.04420.01180.11620.0185-0.031-6.8078-17.3037-4.3581
181.13850.88851.46054.7595-1.73033.89970.5289-0.4723-0.35590.36680.01060.56770.7695-1.0494-0.53950.1096-0.2543-0.0130.15270.0784-0.0105-10.0336-28.51770.5611
196.1249-1.70673.32577.35580.54566.90280.7375-0.614-0.56380.0094-0.16480.75430.5926-0.8481-0.57280.1199-0.2286-0.1875-0.03610.10340.109-8.8069-33.8536-7.9715
2016.03231.052512.87522.7602-2.285622.86470.1082-0.20690.82790.2932-0.11640.29920.2567-1.69940.00830.0727-0.1911-0.10380.00940.0714-0.057-10.9331-26.7777-14.012
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
11524 - 5281 - 5
22529 - 5456 - 22
33546 - 55823 - 35
44559 - 56736 - 44
55568 - 57345 - 50
66574 - 59451 - 71
77595 - 60272 - 79
88603 - 61080 - 87
99611 - 61888 - 95
1010619 - 62596 - 102
1111626 - 634103 - 111
1212635 - 645112 - 122
1313646 - 651123 - 128
1414652 - 659129 - 136
1515660 - 671137 - 148
1616672 - 679149 - 156
1717680 - 685157 - 162
1818686 - 693163 - 170
1919694 - 705171 - 182
2020706 - 711183 - 188

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