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- PDB-3fan: Crystal structure of chymotrypsin-like protease/proteinase (3CLSP... -

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Basic information

Entry
Database: PDB / ID: 3fan
TitleCrystal structure of chymotrypsin-like protease/proteinase (3CLSP/Nsp4) of porcine reproductive and respiratory syndrome virus (PRRSV)
ComponentsNon-structural proteinViral nonstructural protein
KeywordsHYDROLASE / chymotrypsin-like / N-terminal beta-barrels / C-terminal alpha-beta extra domain / canonical catalytic triad
Function / homology
Function and homology information


: / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / host cell nucleus / proteolysis ...: / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / host cell nucleus / proteolysis / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Chymotrypsin-like serine protease; domain 3 / Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain ...Chymotrypsin-like serine protease; domain 3 / Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 / Equine arteritis virus peptidase S32 / Serine protease, chymotrypsin-like serine protease, C-terminal / Arterivirus NSP4 peptidase domain / Arterivirus papain-like cysteine protease beta (PCPbeta) domain / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp7 alpha superfamily / Equine arterivirus Nsp2-type cysteine proteinase / Equine arteritis virus serine endopeptidase S32 / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp4 proteinase domain profile. / Arterivirus nsp2 cysteine protease (AV CP) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain profile. / Arterivirus papain-like cysteine protease beta (PCPbeta) domain profile. / Herpes Virus-1 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Non-structural protein
Similarity search - Component
Biological speciesPorcine respiratory and reproductive syndrome virus
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.9 Å
AuthorsGao, F. / Peng, H. / Tian, X. / Lu, G. / Liu, Y. / Gao, G.F.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and cleavage specificity of the chymotrypsin-like serine protease (3CLSP/nsp4) of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV).
Authors: Tian, X. / Lu, G. / Gao, F. / Peng, H. / Feng, Y. / Ma, G. / Bartlam, M. / Tian, K. / Yan, J. / Hilgenfeld, R. / Gao, G.F.
History
DepositionNov 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Non-structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0972
Polymers22,0021
Non-polymers951
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Non-structural protein
hetero molecules

A: Non-structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1944
Polymers44,0042
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2320 Å2
ΔGint-28 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.358, 49.162, 42.907
Angle α, β, γ (deg.)90.00, 110.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-structural protein / Viral nonstructural protein / Proteinase / 3C like serine protease


Mass: 22001.896 Da / Num. of mol.: 1 / Fragment: UniProt residues 1780-1983
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine respiratory and reproductive syndrome virus
Strain: JXA1 / Gene: Nsp4, ORF1a / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1E8J1, EC: 3.4.21.114
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1M sodium citrate pH 5.3, 0.7M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418, 0.9793, 0.9000
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 15, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97931
30.91
ReflectionResolution: 1.9→32.3 Å / Num. obs: 17461 / Redundancy: 4.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 22.1
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→27.91 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.671 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24585 830 5.1 %RANDOM
Rwork0.19353 ---
obs0.19633 15507 93.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.137 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 5 208 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221427
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.951936
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09824.80852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8815215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.365154
X-RAY DIFFRACTIONr_chiral_restr0.1070.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.2647
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2969
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1211.5970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76921506
X-RAY DIFFRACTIONr_scbond_it2.4943524
X-RAY DIFFRACTIONr_scangle_it3.9894.5430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 55 -
Rwork0.23 1089 -
obs--90.22 %

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