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- PDB-6imp: Crystal structure of alpha-beta hydrolase (ABH) from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 6imp
TitleCrystal structure of alpha-beta hydrolase (ABH) from Vibrio vulnificus
ComponentsRTX toxin RtxA
KeywordsTOXIN / Virulence / hydrolase / alpha-beta fold / toxins
Function / homology
Function and homology information


host cell cytosol / cysteine-type peptidase activity / toxin activity / transferase activity / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
: / : / Pasteurella multocida toxin, C2 domain / C-terminal repeat from RTX toxins / RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily ...: / : / Pasteurella multocida toxin, C2 domain / C-terminal repeat from RTX toxins / RtxA toxin / RtxA repeat / 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. / Serine aminopeptidase, S33 / Serralysin-like metalloprotease, C-terminal / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Autotransporter adhesin
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.62 Å
AuthorsKim, M.H. / Hwang, J.
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 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: RTX toxin RtxA
B: RTX toxin RtxA


Theoretical massNumber of molelcules
Total (without water)68,9132
Polymers68,9132
Non-polymers00
Water37821
1
A: RTX toxin RtxA


Theoretical massNumber of molelcules
Total (without water)34,4561
Polymers34,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RTX toxin RtxA


Theoretical massNumber of molelcules
Total (without water)34,4561
Polymers34,4561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.106, 99.681, 164.890
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 RTX toxin RtxA


Mass: 34456.352 Da / Num. of mol.: 2 / Fragment: Hydrolase fold domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q0KY79*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence has been deposited to database with accession ID WP_015728045.1.

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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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium formate, 25% PEG 3350 / PH range: 7

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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: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22210 / % possible obs: 98.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 23.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.87 / Rsym value: 0.597 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.62→49.84 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / ESU R: 0.669 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28701 1071 4.8 %RANDOM
Rwork0.23724 ---
obs0.23986 21082 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.547 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0 Å2
2---0.12 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.62→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 0 21 4298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9715856
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8385560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18325.222203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42815752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3721524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213313
X-RAY DIFFRACTIONr_gen_planes_other
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_it6.6669.0652252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.93213.5752808
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.3269.4052092
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined14.80175.2346577
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 71 -
Rwork0.42 1366 -
obs--88.76 %

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