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- PDB-3r0f: Human enterovirus 71 3C protease mutant H133G in complex with rup... -

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Basic information

Entry
Database: PDB / ID: 3r0f
TitleHuman enterovirus 71 3C protease mutant H133G in complex with rupintrivir
Components3C protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / chymotrypsin-fold / beta-ribbon / hydrolysis / nucleus / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / proteolysis / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-AG7 / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus 71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3083 Å
AuthorsWang, J. / Fan, T. / Yao, X. / Wu, Z. / Guo, L. / Lei, X. / Wang, J. / Wang, M. / Jin, Q. / Cui, S.
CitationJournal: J.Virol. / Year: 2011
Title: Crystal Structures of Enterovirus 71 3C Protease Complexed with Rupintrivir Reveal the Roles of Catalytically Important Residues.
Authors: Wang, J. / Fan, T. / Yao, X. / Wu, Z. / Guo, L. / Lei, X. / Wang, J. / Wang, M. / Jin, Q. / Cui, S.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Structure summary
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3May 6, 2015Group: Structure summary
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: 3C protein
B: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4938
Polymers41,0432
Non-polymers1,4506
Water5,278293
1
A: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2464
Polymers20,5221
Non-polymers7253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2464
Polymers20,5221
Non-polymers7253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.716, 98.203, 102.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-255-

HOH

21B-283-

HOH

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Components

#1: Protein 3C protein / 3C protease


Mass: 20521.510 Da / Num. of mol.: 2 / Mutation: H133G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus 71 / Strain: 71 / Gene: polyprotein / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta / References: UniProt: E7E815
#2: Chemical ChemComp-AG7 / 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER / RUPINTRIVIR, bound form


Mass: 600.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H41FN4O7 / Comment: antivirus, protease inhibitor*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: Tris-HCl 0.1M, PEG1000 26%, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2010 / Details: Bartels Monochromator
RadiationMonochromator: Double Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.308→57.67 Å / Num. obs: 83287 / % possible obs: 98.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.74 % / Biso Wilson estimate: 19.351 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.78
Reflection shellResolution: 1.308→1.39 Å / Redundancy: 3.36 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.55 / Num. unique all: 12796 / % possible all: 94

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERv2.1phasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSpackagedata reduction
XDSpackagedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CQQ

1cqq


Resolution: 1.3083→57.667 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 16.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1748 7906 4.99 %RANDOM
Rwork0.1475 ---
obs0.1489 158376 96.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.06 Å2 / ksol: 0.434 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7405 Å20 Å2-0 Å2
2--1.2488 Å2-0 Å2
3----1.9893 Å2
Refinement stepCycle: LAST / Resolution: 1.3083→57.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2754 0 102 293 3149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083153
X-RAY DIFFRACTIONf_angle_d1.214296
X-RAY DIFFRACTIONf_dihedral_angle_d15.4871311
X-RAY DIFFRACTIONf_chiral_restr0.097491
X-RAY DIFFRACTIONf_plane_restr0.008554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3083-1.32320.26262120.23563921X-RAY DIFFRACTION75
1.3232-1.33870.23912630.22155034X-RAY DIFFRACTION96
1.3387-1.35510.26292530.20874976X-RAY DIFFRACTION96
1.3551-1.37220.25272560.21454899X-RAY DIFFRACTION94
1.3722-1.39030.27472660.2154917X-RAY DIFFRACTION94
1.3903-1.40930.27412640.20055005X-RAY DIFFRACTION97
1.4093-1.42950.23762670.18295059X-RAY DIFFRACTION98
1.4295-1.45080.22752720.18925124X-RAY DIFFRACTION98
1.4508-1.47350.24122670.18195036X-RAY DIFFRACTION98
1.4735-1.49760.21772680.1755097X-RAY DIFFRACTION98
1.4976-1.52350.20422720.16465125X-RAY DIFFRACTION97
1.5235-1.55120.18272650.15255054X-RAY DIFFRACTION97
1.5512-1.5810.17722640.13885041X-RAY DIFFRACTION97
1.581-1.61330.19462530.14184863X-RAY DIFFRACTION95
1.6133-1.64830.17652690.1245127X-RAY DIFFRACTION98
1.6483-1.68670.17052740.12255116X-RAY DIFFRACTION99
1.6867-1.72890.1672650.11885093X-RAY DIFFRACTION99
1.7289-1.77560.16322750.1175148X-RAY DIFFRACTION98
1.7756-1.82790.16132610.11415095X-RAY DIFFRACTION98
1.8279-1.88690.1412670.11245075X-RAY DIFFRACTION97
1.8869-1.95430.13612530.10444950X-RAY DIFFRACTION96
1.9543-2.03260.14832690.10975006X-RAY DIFFRACTION95
2.0326-2.12510.1182670.10335126X-RAY DIFFRACTION99
2.1251-2.23710.13092690.11275137X-RAY DIFFRACTION99
2.2371-2.37730.13922720.11225131X-RAY DIFFRACTION98
2.3773-2.56080.14842660.12225049X-RAY DIFFRACTION97
2.5608-2.81850.17232580.13814990X-RAY DIFFRACTION95
2.8185-3.22640.14852580.14525025X-RAY DIFFRACTION97
3.2264-4.06470.1612740.13875168X-RAY DIFFRACTION99
4.0647-57.7230.19052670.18185083X-RAY DIFFRACTION97

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