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- PDB-5n8x: Trigonal structure of mutant V173I of 3D polymerase from Foot-and... -

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Basic information

Entry
Database: PDB / ID: 5n8x
TitleTrigonal structure of mutant V173I of 3D polymerase from Foot-and-Mouth Disease Virus
Components3D polymerase
KeywordsVIRAL PROTEIN / 3Dpolymerase / RNA dependent RNA polymerases / 5'-fluoracil / nucleotide analogues
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 / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...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 / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFerrer-Orta, C. / Verdaguer, N.
CitationJournal: Genome Biol Evol / Year: 2017
Title: Molecular and Functional Bases of Selection against a Mutation Bias in an RNA Virus.
Authors: de la Higuera, I. / Ferrer-Orta, C. / de Avila, A.I. / Perales, C. / Sierra, M. / Singh, K. / Sarafianos, S.G. / Dehouck, Y. / Bastolla, U. / Verdaguer, N. / Domingo, E.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3D polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6407
Polymers54,1241
Non-polymers5156
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, In solution is a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-7 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.506, 93.506, 99.626
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 3D polymerase


Mass: 54124.367 Da / Num. of mol.: 1 / Mutation: V173I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Gene: CDS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4H1Z0, UniProt: P03311*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 36% PEG 4000, 0.2M ammonium acetate 0.1M MES(2-(N-morpholino) ethanesulfonic acid) pH 6.0 4% gamma-butyrolactone.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→46.75 Å / Num. obs: 20009 / % possible obs: 96.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 22
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2782 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
REFMACrigid body refinementphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNR

1wnr


Resolution: 2.4→46.75 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.913 / SU B: 26.761 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28149 991 5 %RANDOM
Rwork0.25156 ---
obs0.25298 18995 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.4→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 31 32 3806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193821
X-RAY DIFFRACTIONr_bond_other_d0.0020.023509
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9545167
X-RAY DIFFRACTIONr_angle_other_deg0.96938119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36723.481181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01715625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9961527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02815
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1243.2591882
X-RAY DIFFRACTIONr_mcbond_other0.1243.2581881
X-RAY DIFFRACTIONr_mcangle_it0.2374.8862349
X-RAY DIFFRACTIONr_mcangle_other0.2374.8872350
X-RAY DIFFRACTIONr_scbond_it0.0453.2981938
X-RAY DIFFRACTIONr_scbond_other0.0463.2981938
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1044.9232819
X-RAY DIFFRACTIONr_long_range_B_refined1.56461.24615560
X-RAY DIFFRACTIONr_long_range_B_other1.56461.24415560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 59 -
Rwork0.331 1311 -
obs--94.09 %
Refinement TLS params.Method: refined / Origin x: 18.2996 Å / Origin y: 26.6133 Å / Origin z: 23.7697 Å
111213212223313233
T0.1279 Å2-0.0451 Å2-0.0203 Å2-0.2534 Å2-0.0179 Å2--0.2908 Å2
L1.2458 °2-0.6897 °21.1271 °2-5.9471 °2-1.4837 °2--2.192 °2
S-0.1098 Å °0.084 Å °0.0357 Å °-0.4884 Å °0.2662 Å °0.4821 Å °0.1077 Å °-0.3483 Å °-0.1565 Å °

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