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- PDB-1qmy: FMDV LEADER PROTEASE (LBSHORT-C51A-C133S) -

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Basic information

Entry
Database: PDB / ID: 1qmy
TitleFMDV LEADER PROTEASE (LBSHORT-C51A-C133S)
ComponentsPROTEASE
KeywordsHYDROLASE / SULFHYDRYL PROTEINASE / PICORNAVIRAL PROTEINASE
Function / homology
Function and homology information


L-peptidase / suppression by virus of host type I interferon production / modulation by virus 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 ...L-peptidase / suppression by virus of host type I interferon production / modulation by virus 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 / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / molecular adaptor activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Cysteine proteinases / Cathepsin B; Chain A ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Cysteine proteinases / Cathepsin B; Chain A / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Biological speciesAPHTHOVIRUS O
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuarne, A. / Tormo, J. / Glaser, W. / Skern, T. / Fita, I.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure and Biochemical Features Distinguish the Foot-and-Mouth Disease Virus Leader Proteinase from Other Papain-Like Enzymes
Authors: Guarne, A. / Hampoelz, B. / Glaser, W. / Carpena, X. / Tormo, J. / Fita, I. / Skern, T.
History
DepositionOct 8, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE
B: PROTEASE
C: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1465
Polymers57,0223
Non-polymers1242
Water7,548419
1
A: PROTEASE


Theoretical massNumber of molelcules
Total (without water)19,0071
Polymers19,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1313
Polymers19,0071
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PROTEASE


Theoretical massNumber of molelcules
Total (without water)19,0071
Polymers19,0071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.064, 110.751, 56.966
Angle α, β, γ (deg.)90.00, 98.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEASE / / LEADER PROTEASE


Mass: 19007.182 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APHTHOVIRUS O / Strain: O1K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03305
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SWISSPROT ENTRY POLG_FMDVO REFERS TO A GENOME POLYPROTEIN, AND THE PROTEASE (EC 3.4.22.-) ...THE SWISSPROT ENTRY POLG_FMDVO REFERS TO A GENOME POLYPROTEIN, AND THE PROTEASE (EC 3.4.22.-) LISTED IS FOR THE RESIDUES 1650 TO 1862. THE PROTEASE STUDIED HERE WAS FOUND IN THE RESIDUES 29 TO 195 THAT ARE LISTED IN SWISSPROT AS A NONSTRUCTURAL PROTEIN P20A.

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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: 2.5 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.5
Details: 20% PEG 8000, 0.2 M MG ACETATE, 0.1 M NA CACODYLATE, PH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8469
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8469 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 42246 / % possible obs: 95 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.032 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.215 / % possible all: 93
Reflection
*PLUS
Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.215

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1253445.97 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2977 7.1 %RANDOM
Rwork0.19 ---
obs0.19 42222 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54 Å2 / ksol: 0.373411 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.2 Å20 Å2-2.52 Å2
2--2.41 Å20 Å2
3---1.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 8 419 4189
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.171.5
X-RAY DIFFRACTIONc_mcangle_it32
X-RAY DIFFRACTIONc_scbond_it2.952
X-RAY DIFFRACTIONc_scangle_it3.992.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 506 7.3 %
Rwork0.232 6419 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ETH.PARETH.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11

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