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- PDB-3sj8: Crystal structure of the 3C protease from coxsackievirus A16 -

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Basic information

Entry
Database: PDB / ID: 3sj8
TitleCrystal structure of the 3C protease from coxsackievirus A16
Components3C protease
KeywordsHYDROLASE / chymotrypsin-like fold / protease
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 ...Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman coxsackievirus A16
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsLu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2011
Title: Enterovirus 71 and Coxsackievirus A16 3C Proteases: Binding to Rupintrivir and Their Substrates and Anti-Hand, Foot, and Mouth Disease Virus Drug Design.
Authors: Lu, G. / Qi, J. / Chen, Z. / Xu, X. / Gao, F. / Lin, D. / Qian, W. / Liu, H. / Jiang, H. / Yan, J. / Gao, G.F.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C protease


Theoretical massNumber of molelcules
Total (without water)21,0901
Polymers21,0901
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.586, 40.586, 99.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein 3C protease


Mass: 21090.186 Da / Num. of mol.: 1 / Fragment: UNP residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coxsackievirus A16 / Strain: Beijing0907 / Gene: 3C / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C8CIL7, picornain 3C
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 0.1 M ammonium acetate, 17% w/v PEG10000, 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
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 25, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.199→50 Å / Num. all: 8223 / Num. obs: 8199 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 21.067
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.357 / Num. unique all: 818 / Rsym value: 0.51 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZTY

2zty


Resolution: 2.199→17.3 Å / SU ML: 0.25 / σ(F): 0.2 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 361 4.66 %RANDOM
Rwork0.1919 ---
obs0.1937 7750 94.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.534 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5478 Å20 Å2-0 Å2
2--3.5478 Å20 Å2
3----7.0956 Å2
Refinement stepCycle: LAST / Resolution: 2.199→17.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 0 75 1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141413
X-RAY DIFFRACTIONf_angle_d1.3581912
X-RAY DIFFRACTIONf_dihedral_angle_d20.737516
X-RAY DIFFRACTIONf_chiral_restr0.174221
X-RAY DIFFRACTIONf_plane_restr0.004247
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1986-2.51590.26571200.23432340234090
2.5159-3.16660.23771030.2042475247595
3.1666-17.30040.21251380.17482574257499
Refinement TLS params.Method: refined / Origin x: -20.6269 Å / Origin y: 0.1343 Å / Origin z: 0.0294 Å
111213212223313233
T0.0597 Å2-0.0017 Å20.0056 Å2-0.1813 Å20.0257 Å2--0.1328 Å2
L0.6991 °2-0.1336 °2-0.3983 °2-1.7698 °2-0.6907 °2--2.995 °2
S-0.049 Å °0.0474 Å °0.0447 Å °0.0623 Å °-0.0233 Å °-0.0347 Å °0.0214 Å °0.344 Å °0.0582 Å °
Refinement TLS groupSelection details: all

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