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- PDB-3sj9: crystal structure of the C147A mutant 3C of CVA16 in complex with... -

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Basic information

Entry
Database: PDB / ID: 3sj9
Titlecrystal structure of the C147A mutant 3C of CVA16 in complex with FAGLRQAVTQ peptide
Components
  • 3C proteasePicornain 3C
  • FAGLRQAVTQ peptide
KeywordsHYDROLASE / binding to its substrate-peptide / chymotrypsin-like fold / protease
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / proteolysis / RNA binding ...T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / 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: 2.399 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
B: FAGLRQAVTQ peptide


Theoretical massNumber of molelcules
Total (without water)22,1492
Polymers22,1492
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-3 kcal/mol
Surface area8910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.519, 62.519, 110.093
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 3C protease / Picornain 3C


Mass: 21058.121 Da / Num. of mol.: 1 / Fragment: UNP residues 1-183 / Mutation: C147A
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: Protein/peptide FAGLRQAVTQ peptide


Mass: 1091.240 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.2 M lithium sulfate, 25% w/v PEG3350, 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: Oct 28, 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: 2.399→50 Å / Num. all: 9118 / Num. obs: 9106 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/σ(I): 20.158
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 5.067 / Num. unique all: 885 / Rsym value: 0.576 / % possible all: 100

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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 3SJ8

3sj8


Resolution: 2.399→27.523 Å / SU ML: 0.31 / σ(F): 0.26 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 424 4.87 %RANDOM
Rwork0.1949 ---
obs0.1971 8714 96.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.605 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6841 Å2-0 Å20 Å2
2---1.6841 Å2-0 Å2
3---3.3683 Å2
Refinement stepCycle: LAST / Resolution: 2.399→27.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 0 111 1558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081472
X-RAY DIFFRACTIONf_angle_d0.7581991
X-RAY DIFFRACTIONf_dihedral_angle_d20.178538
X-RAY DIFFRACTIONf_chiral_restr0.057231
X-RAY DIFFRACTIONf_plane_restr0.003258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.399-2.74580.29831440.23592621262194
2.7458-3.45840.2311370.19912725272596
3.4584-27.5250.22441430.17442944294498
Refinement TLS params.Method: refined / Origin x: -8.346 Å / Origin y: -14.8711 Å / Origin z: -18.8853 Å
111213212223313233
T0.1015 Å2-0.012 Å2-0.0051 Å2-0.0744 Å20.0012 Å2--0.0845 Å2
L0.5841 °2-0.0719 °20.1725 °2-0.8519 °20.2928 °2--0.3638 °2
S-0.0396 Å °0.0409 Å °0.0302 Å °-0.0365 Å °0.0526 Å °-0.0265 Å °-0.0154 Å °0.0019 Å °-0 Å °
Refinement TLS groupSelection details: all

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