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- PDB-6ii0: Crystal structure of the Makes Caterpillars Floppy (MCF)-Like eff... -

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Basic information

Entry
Database: PDB / ID: 6ii0
TitleCrystal structure of the Makes Caterpillars Floppy (MCF)-Like effector of Vibrio vulnificus MO6-24/O
ComponentsPutative RTX-toxin
KeywordsTOXIN / MCF / MARTX TOXIN / EFFECTOR DOMAIN
Function / homology
Function and homology information


host cell cytosol / toxin activity / transferase activity / cysteine-type endopeptidase activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
: / Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / alpha/beta hydrolase fold ...: / Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLee, Y. / Kim, B.S. / Choi, S. / Lee, E.Y. / Park, S. / Hwang, J. / Kwon, Y. / Hyun, J. / Lee, C. / Eom, S.H. / Kim, M.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Makes caterpillars floppy-like effector-containing MARTX toxins require host ADP-ribosylation factor (ARF) proteins for systemic pathogenicity.
Authors: Lee, Y. / Kim, B.S. / Choi, S. / Lee, E.Y. / Park, S. / Hwang, J. / Kwon, Y. / Hyun, J. / Lee, C. / Kim, J.F. / Eom, S.H. / Kim, M.H.
History
DepositionOct 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative RTX-toxin
B: Putative RTX-toxin
C: Putative RTX-toxin
D: Putative RTX-toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,3775
Polymers163,2854
Non-polymers921
Water6,539363
1
A: Putative RTX-toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9132
Polymers40,8211
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area17780 Å2
MethodPISA
2
B: Putative RTX-toxin


Theoretical massNumber of molelcules
Total (without water)40,8211
Polymers40,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17960 Å2
MethodPISA
3
C: Putative RTX-toxin


Theoretical massNumber of molelcules
Total (without water)40,8211
Polymers40,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16940 Å2
MethodPISA
4
D: Putative RTX-toxin


Theoretical massNumber of molelcules
Total (without water)40,8211
Polymers40,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.640, 78.640, 450.008
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Putative RTX-toxin


Mass: 40821.262 Da / Num. of mol.: 4 / Fragment: MCF / Mutation: C3351S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: rtxA1 / Production host: Escherichia coli (E. coli) / References: UniProt: F1CLG9*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence has been deposited to database with NCBI accession ID WP_015728045.1. GAM at N- ...The sequence has been deposited to database with NCBI accession ID WP_015728045.1. GAM at N-terminal were from expression tag. Residue C3351S represents mutation.

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 12% PEG 3000, 0.1M Na2HPO4/citric acid (pH 4.2), 0.4M NaCl, 10% glycerol

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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: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.36→50 Å / Num. obs: 60806 / % possible obs: 97.3 % / Redundancy: 5 % / Net I/σ(I): 6.1
Reflection shellResolution: 2.36→2.4 Å / Num. unique obs: 3219 / CC1/2: 0.77 / Rpim(I) all: 0.273 / Rrim(I) all: 0.643

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6II6

6ii6


Resolution: 2.36→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.317 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.235 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23662 3193 5.1 %RANDOM
Rwork0.18242 ---
obs0.18517 59323 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.146 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.36→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9567 0 6 363 9936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199762
X-RAY DIFFRACTIONr_bond_other_d0.0060.029095
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.97413174
X-RAY DIFFRACTIONr_angle_other_deg0.83321165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16751249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16325.499431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.994151611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911537
X-RAY DIFFRACTIONr_chiral_restr0.0840.21458
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021898
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_it3.6313.7045005
X-RAY DIFFRACTIONr_mcbond_other3.633.7035004
X-RAY DIFFRACTIONr_mcangle_it5.6815.5326251
X-RAY DIFFRACTIONr_mcangle_other5.685.5336252
X-RAY DIFFRACTIONr_scbond_it4.3564.2064757
X-RAY DIFFRACTIONr_scbond_other4.3544.2064757
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5576.0726924
X-RAY DIFFRACTIONr_long_range_B_refined9.41144.33910998
X-RAY DIFFRACTIONr_long_range_B_other9.4144.34210999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.421 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 237 -
Rwork0.246 4456 -
obs--99.11 %

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