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- PDB-1wqs: Crystal structure of Norovirus 3C-like protease -

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Basic information

Entry
Database: PDB / ID: 1wqs
TitleCrystal structure of Norovirus 3C-like protease
Components3C-like protease
KeywordsHYDROLASE / NOROVIRUS / 3C-LIKE PROTEASE / CHYMOTRYPSIN LIKE PROTEASE / OXYANION HOLE / NORWALK-LIKE VIRUS
Function / homology
Function and homology information


calicivirin / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases ...Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
: / D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / NTPase
Similarity search - Component
Biological speciesChiba virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsNakamura, K. / Someya, Y. / Kumasaka, T. / Tanaka, N.
CitationJournal: J.Virol. / Year: 2005
Title: A norovirus protease structure provides insights into active and substrate binding site integrity
Authors: Nakamura, K. / Someya, Y. / Kumasaka, T. / Ueno, G. / Yamamoto, M. / Sato, T. / Takeda, N. / Miyamura, T. / Tanaka, N.
History
DepositionOct 1, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like protease
B: 3C-like protease
C: 3C-like protease
D: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,22714
Polymers74,3224
Non-polymers1,90510
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-155 kcal/mol
Surface area27600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.890, 128.890, 118.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
3C-like protease /


Mass: 18580.516 Da / Num. of mol.: 4 / Fragment: residues 1-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chiba virus / Genus: Norovirus / Species: Norwalk virusNorovirus / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon-Plus / References: UniProt: Q9DU47
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.77 Å3/Da / Density % sol: 67.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: POTASSIUM SODIUM TARTRATE TETRAHYDRATE, SODIUM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.0050, 1.0091, 1.0013, 0.9800
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0051
21.00911
31.00131
40.981
ReflectionResolution: 2.8→43.53 Å / Num. all: 53872 / % possible obs: 99.8 % / Redundancy: 2.76 % / Biso Wilson estimate: 2.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5367 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2208257.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2602 10 %RANDOM
Rwork0.206 ---
obs0.206 26258 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 146.829 Å2 / ksol: 0.574687 e/Å3
Displacement parametersBiso mean: 66.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å24.48 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 28 127 5367
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.052
X-RAY DIFFRACTIONc_angle_deg4.9
X-RAY DIFFRACTIONc_dihedral_angle_d29.8
X-RAY DIFFRACTIONc_improper_angle_d4.3
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 419 9.7 %
Rwork0.299 3913 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4TAR.PARAM

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