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- PDB-2j92: 3C PROTEASE FROM TYPE A10(61) FOOT-AND-MOUTH DISEASE VIRUS - Crys... -

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Basic information

Entry
Database: PDB / ID: 2j92
Title3C PROTEASE FROM TYPE A10(61) FOOT-AND-MOUTH DISEASE VIRUS - Crystal packing mutant (K51Q)
ComponentsPICORNAIN 3C
KeywordsHYDROLASE / FOOT-AND- MOUTH DISEASE VIRUS / CHYMOTRYPSIN-LIKE CYSTEINE PROTEASE / THIOL PROTEASE / RNA REPLICATION
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / regulation of translation / channel activity / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Papain-like cysteine peptidase superfamily ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / 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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / 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
Biological speciesFOOT-AND-MOUTH DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSweeney, T.R. / Birtley, J.R. / Leatherbarrow, R.J. / Curry, S.
Citation
Journal: J.Virol. / Year: 2007
Title: Structural and Mutagenic Analysis of Foot-and-Mouth Disease Virus 3C Protease Reveals the Role of the {Beta}-Ribbon in Proteolysis.
Authors: Sweeney, T.R. / Roque-Rosell, N. / Birtley, J.R. / Leatherbarrow, R.J. / Curry, S.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease: New Insights Into Catalytic Mechanism and Cleavage Specificity
Authors: Birtley, J.R. / Knox, S.R. / Jaulent, A.M. / Brick, P. / Leatherbarrow, R.J. / Curry, S.
History
DepositionNov 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PICORNAIN 3C
B: PICORNAIN 3C


Theoretical massNumber of molelcules
Total (without water)45,0362
Polymers45,0362
Non-polymers00
Water1,964109
1
A: PICORNAIN 3C


Theoretical massNumber of molelcules
Total (without water)22,5181
Polymers22,5181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PICORNAIN 3C


Theoretical massNumber of molelcules
Total (without water)22,5181
Polymers22,5181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.387, 71.708, 92.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9227, 0.3129, 0.2253), (0.2937, 0.9489, -0.1152), (-0.2499, -0.0401, -0.9674)
Vector: 3.9137, -4.3413, 0.6301)

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Components

#1: Protein PICORNAIN 3C / PROTEASE 3C / P3C / PROTEASE P20B / 3C PROTEASE


Mass: 22518.006 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: K51Q - TO DISRUPT ORIGINAL CRYSTAL PACKING C95K - TO AVOID AGGREGATION C142S - TO AVOID AGGREGATION C163A - TO REMOVE ACITVE-STE NUCLEOPHILE.
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS (STRAIN A10-61)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03306, picornain 3C
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 1700 TO GLN ENGINEERED RESIDUE IN CHAIN A, CYS 1744 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, LYS 1700 TO GLN ENGINEERED RESIDUE IN CHAIN A, CYS 1744 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS 1791 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 1812 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 1700 TO GLN ENGINEERED RESIDUE IN CHAIN B, CYS 1744 TO LYS ENGINEERED RESIDUE IN CHAIN B, CYS 1791 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 1812 TO ALA
Sequence detailsTHE CONFLICT ASN1671 (ILE22) ARISES PROBABLY BECAUSE OF A SEQUENCING ERROR IN THE P03306 ENTRY. ...THE CONFLICT ASN1671 (ILE22) ARISES PROBABLY BECAUSE OF A SEQUENCING ERROR IN THE P03306 ENTRY. COMPARISON OF OVER 40 FMDV 3C SEQUENCES SHOW THAT ILE 22 IS STRICTLY CONSERVED EXCEPT, APPARENTLY, IN P03306

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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: 2.4 Å3/Da / Density % sol: 48.36 %
Crystal growpH: 7 / Details: SEE PAPER, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 2005
Details: RH COATED COLLIMATING MIRROR, A DOUBLE CRYSTAL SI(III) MONOCHROMATOR WITH HORIZONTAL SAGGITAL FOCUSING SYSTEM, AND FINALLY A SECOND RH COATED MIRROR FOR VERTICAL FOCUSING.
RadiationMonochromator: DOUBLE CRYSTAL SI(III) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→23.6 Å / Num. obs: 20590 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BHG

2bhg


Resolution: 2.2→23.59 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1483613.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.254 998 4.9 %RANDOM
Rwork0.229 ---
obs0.229 20549 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.3037 Å2 / ksol: 0.329538 e/Å3
Displacement parametersBiso mean: 34.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.37 Å20 Å20 Å2
2---4.31 Å20 Å2
3----2.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 0 109 2927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 157 4.7 %
Rwork0.386 3190 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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