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- PDB-8yjc: Structure of Vibrio vulnificus MARTX cysteine protease domain C3727A -

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Basic information

Entry
Database: PDB / ID: 8yjc
TitleStructure of Vibrio vulnificus MARTX cysteine protease domain C3727A
ComponentsMultifunctional autoprocessing repeat-in-toxin (MARTX)
KeywordsTOXIN / protease / Inositol hexaphosphate / activation
Function / homologyINOSITOL HEXAKISPHOSPHATE
Function and homology information
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsChen, L. / Khan, H. / Tan, L. / Li, X. / Zhang, G. / Im, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00241410 Korea, Republic Of
CitationJournal: Plos One / Year: 2024
Title: Structural basis of the activation of MARTX cysteine protease domain from Vibrio vulnificus.
Authors: Chen, L. / Khan, H. / Tan, L. / Li, X. / Zhang, G. / Im, Y.J.
History
DepositionMar 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multifunctional autoprocessing repeat-in-toxin (MARTX)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1544
Polymers24,3491
Non-polymers8053
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-13 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.060, 69.816, 40.041
Angle α, β, γ (deg.)90.000, 107.690, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-4046-

HOH

21A-4142-

HOH

31A-4179-

HOH

41A-4184-

HOH

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Components

#1: Protein Multifunctional autoprocessing repeat-in-toxin (MARTX)


Mass: 24348.615 Da / Num. of mol.: 1 / Fragment: cysteine protease domain / Mutation: C3727A
Source method: isolated from a genetically manipulated source
Details: NCBI Reference Sequence: WP_058645630.1, MARTX cysteine protease domain, C3727A mutant. The N-terminal GSAMGS is a linker sequence to the cleavable His-tag by thrombin.
Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Gene: rtxa / Plasmid: pHIS2-thr
Details (production host): the N-terminal thrombin cleavable His-tag fusion
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M HEPES pH 9.0, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 54914 / % possible obs: 97.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 12.96 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 46.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 2163 / % possible all: 76.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→24.73 Å / SU ML: 0.1106 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.8738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1892 1996 3.64 %
Rwork0.1699 52895 -
obs0.1706 54891 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.03 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 45 345 2001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551679
X-RAY DIFFRACTIONf_angle_d0.95812280
X-RAY DIFFRACTIONf_chiral_restr0.0863246
X-RAY DIFFRACTIONf_plane_restr0.0157299
X-RAY DIFFRACTIONf_dihedral_angle_d13.1758229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.21311130.19252978X-RAY DIFFRACTION76
1.33-1.370.20781330.19093553X-RAY DIFFRACTION91.71
1.37-1.410.19321470.17753875X-RAY DIFFRACTION99.65
1.41-1.450.19051440.18043831X-RAY DIFFRACTION99.52
1.45-1.510.21581470.1733876X-RAY DIFFRACTION99.63
1.51-1.570.17391450.16813871X-RAY DIFFRACTION99.63
1.57-1.640.18431460.16263891X-RAY DIFFRACTION99.75
1.64-1.720.18991460.16583891X-RAY DIFFRACTION99.88
1.72-1.830.20241480.17773894X-RAY DIFFRACTION99.8
1.83-1.970.17661460.16823861X-RAY DIFFRACTION99.68
1.97-2.170.20431480.16093921X-RAY DIFFRACTION99.9
2.17-2.490.1821470.17553892X-RAY DIFFRACTION99.95
2.49-3.130.20921480.17433923X-RAY DIFFRACTION99.83
3.13-24.730.16751380.16283638X-RAY DIFFRACTION91.56

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