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- PDB-3ifu: The Crystal Structure of Porcine Reproductive and Respiratory Syn... -

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Basic information

Entry
Database: PDB / ID: 3ifu
TitleThe Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) Leader Protease Nsp1
ComponentsNon-structural proteinViral nonstructural protein
KeywordsTRANSCRIPTION / PRRSV / nsp1 / zinc finger / papain-like cysteine protease
Function / homology
Function and homology information


host cell membrane / helicase activity / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / host cell nucleus / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Porcine arterivirus-type cysteine proteinase alpha domain / Rhinovirus 14, subunit 4 - #390 / 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 ...Porcine arterivirus-type cysteine proteinase alpha domain / Rhinovirus 14, subunit 4 - #390 / 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. / Rhinovirus 14, subunit 4 / Cathepsin B; Chain A / Few Secondary Structures / Irregular / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 6
Similarity search - Component
Biological speciesPorcine reproductive and respiratory syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.42 Å
AuthorsSun, Y. / Xue, F. / Guo, Y. / Ma, M. / Lou, Z. / Rao, Z.
CitationJournal: J.Virol. / Year: 2009
Title: Crystal structure of porcine reproductive and respiratory syndrome virus leader protease Nsp1alpha
Authors: Sun, Y. / Xue, F. / Guo, Y. / Ma, M. / Hao, N. / Zhang, X.C. / Lou, Z. / Li, X. / Rao, Z.
History
DepositionJul 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)20,1163
Polymers19,9851
Non-polymers1312
Water91951
1
A: Non-structural protein
hetero molecules

A: Non-structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2326
Polymers39,9712
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2420 Å2
ΔGint-20 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.000, 51.000, 154.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Non-structural protein / Viral nonstructural protein


Mass: 19985.326 Da / Num. of mol.: 1 / Fragment: Leader Protease Nsp1, residues 1-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus
Gene: ORF1a / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B6VGX5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM Tris-HCl, 25%(v/v) tert-butanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1.2821, 1.2827
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Mar 5, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28211
21.28271
ReflectionResolution: 2.42→50 Å / Num. all: 8281 / Num. obs: 8279 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.42→2.5 Å / Rmerge(I) obs: 0.419 / % possible all: 95

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELXmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.42→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 410 random
Rwork0.223 --
all0.237 8281 -
obs0.231 8269 -
Refinement stepCycle: LAST / Resolution: 2.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1367 0 2 51 1420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.07
X-RAY DIFFRACTIONc_bond_d0.012

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