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- PDB-8yja: Structure of Vibrio vulnificus MARTX cysteine protease domain lac... -

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Basic information

Entry
Database: PDB / ID: 8yja
TitleStructure of Vibrio vulnificus MARTX cysteine protease domain lacking beta-flap
ComponentsMARTX cysteine protease domain
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: 2.2 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: MARTX cysteine protease domain
B: MARTX cysteine protease domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0414
Polymers45,3582
Non-polymers6832
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-35 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.321, 77.321, 118.816
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein MARTX cysteine protease domain


Mass: 22678.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NCBI Reference Sequence: WP_058645630.1. A fragment of MARTX cysteine protease domain lacking the C-terminal beta-flap. The N-terminal GSAMGS is a linker sequence from the plasmid vector for ...Details: NCBI Reference Sequence: WP_058645630.1. A fragment of MARTX cysteine protease domain lacking the C-terminal beta-flap. The N-terminal GSAMGS is a linker sequence from the plasmid vector for the cleavable His-tag.
Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Gene: rtxa / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: .1 M sodium acetate pH 4.0, 25% PEG 3350, 0.2 M ammonium acetate, and 2.5% ethylene glycol

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Data collection

DiffractionMean temperature: 110 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: 2.2→50 Å / Num. obs: 18979 / % possible obs: 99.7 % / Redundancy: 11.6 % / Biso Wilson estimate: 36.53 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 43.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 12 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 7.6 / Num. unique obs: 918 / % possible all: 99.9

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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: 2.2→32.4 Å / SU ML: 0.2673 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.277 1890 10 %
Rwork0.2072 17015 -
obs0.2141 18905 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.58 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2611 0 37 97 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072685
X-RAY DIFFRACTIONf_angle_d0.87093641
X-RAY DIFFRACTIONf_chiral_restr0.0567400
X-RAY DIFFRACTIONf_plane_restr0.0075486
X-RAY DIFFRACTIONf_dihedral_angle_d9.3905362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.34811310.24741184X-RAY DIFFRACTION99.85
2.26-2.320.35091330.24391189X-RAY DIFFRACTION99.92
2.32-2.380.33871330.23491197X-RAY DIFFRACTION99.63
2.38-2.460.2921300.23411175X-RAY DIFFRACTION99.85
2.46-2.550.34581320.24251194X-RAY DIFFRACTION99.77
2.55-2.650.3131340.25251200X-RAY DIFFRACTION99.7
2.65-2.770.30161340.23911210X-RAY DIFFRACTION99.93
2.77-2.920.31061320.23821188X-RAY DIFFRACTION99.85
2.92-3.10.27721360.23521219X-RAY DIFFRACTION100
3.1-3.340.29581340.2151213X-RAY DIFFRACTION100
3.34-3.680.27531380.20611233X-RAY DIFFRACTION99.93
3.68-4.210.25791360.18591230X-RAY DIFFRACTION99.93
4.21-5.290.23241380.17051249X-RAY DIFFRACTION100
5.3-32.40.2441490.18421334X-RAY DIFFRACTION98.87

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