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- PDB-3mmg: Crystal structure of tobacco vein mottling virus protease -

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Basic information

Entry
Database: PDB / ID: 3mmg
TitleCrystal structure of tobacco vein mottling virus protease
Components
  • Nuclear inclusion protein A
  • Nuclear inclusion protein B fragment
KeywordsVIRAL PROTEIN / HYDROLASE / 3C-type protease / TEV / TVMV
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / RNA-protein covalent cross-linking / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / cysteine-type peptidase activity / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA-directed RNA polymerase ...nuclear-inclusion-a endopeptidase / helper-component proteinase / RNA-protein covalent cross-linking / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / cysteine-type peptidase activity / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Peptidase family C4 / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / 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
FORMIC ACID / Genome polyprotein / Nuclear inclusion protein A
Similarity search - Component
Biological speciesTobacco vein mottling virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPing, S. / Austin, B.P. / Tozser, J. / Waugh, D.S.
CitationJournal: Protein Sci. / Year: 2010
Title: Structural determinants of tobacco vein mottling virus protease substrate specificity.
Authors: Sun, P. / Austin, B.P. / Tozser, J. / Waugh, D.S.
History
DepositionApr 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Nuclear inclusion protein A
B: Nuclear inclusion protein A
C: Nuclear inclusion protein B fragment
D: Nuclear inclusion protein B fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1405
Polymers56,0944
Non-polymers461
Water9,962553
1
A: Nuclear inclusion protein A
C: Nuclear inclusion protein B fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0933
Polymers28,0472
Non-polymers461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-7 kcal/mol
Surface area11330 Å2
MethodPISA
2
B: Nuclear inclusion protein A
D: Nuclear inclusion protein B fragment


Theoretical massNumber of molelcules
Total (without water)28,0472
Polymers28,0472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-6 kcal/mol
Surface area10640 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-26 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.476, 77.563, 78.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear inclusion protein A


Mass: 27064.793 Da / Num. of mol.: 2 / Mutation: K65A, K67A, C151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco vein mottling virus / Gene: protease / Plasmid: pDESTHisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL (DE3) / References: UniProt: Q9J0W2, UniProt: P09814*PLUS
#2: Protein/peptide Nuclear inclusion protein B fragment


Mass: 982.026 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Peptide 8mer / Source: (synth.) Tobacco vein mottling virus / References: UniProt: P09814*PLUS
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium formate 20% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 25, 2007
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.7→35 Å / Num. all: 50064 / Num. obs: 50064 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.7 / % possible all: 92.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q31

1q31


Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.032 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20961 2544 5.1 %RANDOM
Rwork0.17456 ---
obs0.17634 47451 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.435 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3540 0 3 553 4096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223688
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9254997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62124.32169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84515628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8131516
X-RAY DIFFRACTIONr_chiral_restr0.10.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022804
X-RAY DIFFRACTIONr_nbd_refined0.2060.21667
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2421
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.241
X-RAY DIFFRACTIONr_mcbond_it0.951.52318
X-RAY DIFFRACTIONr_mcangle_it1.51923674
X-RAY DIFFRACTIONr_scbond_it2.30731547
X-RAY DIFFRACTIONr_scangle_it3.6154.51323
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 191 -
Rwork0.242 3278 -
obs--91.6 %

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