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- PDB-6a8j: Crystal structure of bacterial protein toxins -

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Basic information

Entry
Database: PDB / ID: 6a8j
TitleCrystal structure of bacterial protein toxins
ComponentsRTX toxin
KeywordsTOXIN / protein toxin / virulence
Function / homology
Function and homology information


host cell membrane / toxin activity / extracellular region / membrane
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #180 / Rossmann fold - #11550 / : / Pasteurella multocida toxin, C2 domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #180 / Rossmann fold - #11550 / : / Pasteurella multocida toxin, C2 domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio vulnificus CMCP6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.711 Å
AuthorsKim, M.H. / Hwang, J. / Jang, S.Y.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis of inactivation of Ras and Rap1 small GTPases by Ras/Rap1-specific endopeptidase from the sepsis-causing pathogenVibrio vulnificus
Authors: Jang, S.Y. / Hwang, J. / Kim, B.S. / Lee, E.Y. / Oh, B.H. / Kim, M.H.
History
DepositionJul 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Mar 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,74916
Polymers210,6004
Non-polymers1,14912
Water4,414245
1
A: RTX toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8423
Polymers52,6501
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RTX toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1266
Polymers52,6501
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RTX toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9384
Polymers52,6501
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RTX toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8423
Polymers52,6501
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.686, 197.928, 163.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-4212-

HOH

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Components

#1: Protein
RTX toxin


Mass: 52650.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus CMCP6 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSP0*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence has been deposited to database with accession number WP_011081430. N-terminal residues ...The sequence has been deposited to database with accession number WP_011081430. N-terminal residues GAMA are from expression tag.

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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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.4 M ammonium sulfate, 0.1 M Tris-HCl (pH 8.0), 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 135922 / % possible obs: 94.52 % / Redundancy: 6.6 % / Net I/σ(I): 17.27
Reflection shellResolution: 2.7→2.71 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.711→31.706 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 3708 5.04 %
Rwork0.2263 --
obs0.2283 73561 94.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.711→31.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14584 0 61 245 14890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214873
X-RAY DIFFRACTIONf_angle_d0.50720077
X-RAY DIFFRACTIONf_dihedral_angle_d10.4295482
X-RAY DIFFRACTIONf_chiral_restr0.022226
X-RAY DIFFRACTIONf_plane_restr0.0022628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7113-2.7470.3459880.30271742X-RAY DIFFRACTION63
2.747-2.78460.33851370.32672551X-RAY DIFFRACTION91
2.7846-2.82430.39311310.32162620X-RAY DIFFRACTION91
2.8243-2.86650.33721330.32382607X-RAY DIFFRACTION93
2.8665-2.91120.3491420.32212632X-RAY DIFFRACTION93
2.9112-2.95890.34461440.30682630X-RAY DIFFRACTION93
2.9589-3.00990.35531270.30592692X-RAY DIFFRACTION95
3.0099-3.06460.38781280.29722700X-RAY DIFFRACTION95
3.0646-3.12350.29351560.27862689X-RAY DIFFRACTION96
3.1235-3.18720.32811360.27862712X-RAY DIFFRACTION96
3.1872-3.25640.31011450.26792717X-RAY DIFFRACTION96
3.2564-3.33210.3251470.25652719X-RAY DIFFRACTION96
3.3321-3.41530.29371560.24052670X-RAY DIFFRACTION95
3.4153-3.50760.24231610.2322707X-RAY DIFFRACTION95
3.5076-3.61060.261440.22462674X-RAY DIFFRACTION95
3.6106-3.7270.25731250.21872776X-RAY DIFFRACTION97
3.727-3.860.2591270.20652719X-RAY DIFFRACTION96
3.86-4.01420.2291440.19972720X-RAY DIFFRACTION95
4.0142-4.19650.23031310.19282726X-RAY DIFFRACTION95
4.1965-4.41720.20361470.1822797X-RAY DIFFRACTION98
4.4172-4.69320.22431540.17742754X-RAY DIFFRACTION97
4.6932-5.05420.21021590.16782785X-RAY DIFFRACTION98
5.0542-5.56040.24331620.20122836X-RAY DIFFRACTION98
5.5604-6.35930.28321700.21522825X-RAY DIFFRACTION99
6.3593-7.99080.24441530.19362878X-RAY DIFFRACTION99
7.9908-31.70790.19121610.16872975X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.431-1.34052.31570.3792-0.71011.26460.36060.8287-0.495-0.15650.09410.3143-0.4694-0.6736-0.40940.37570.07820.00110.8078-0.05080.5775-76.0794-55.04671.3589
2-0.0398-0.2597-0.12035.36563.5292.48680.02010.08-0.003-0.4427-0.29190.67790.1031-0.27310.22730.4553-0.0480.01510.2241-0.01060.2851-52.1279-73.0135-4.4543
32.29720.87520.59743.63621.01831.21750.1239-0.03130.03980.0916-0.0365-0.57680.16550.1956-0.07050.52560.04830.0150.15710.03210.2127-27.0229-76.54596.8318
47.0220.6629-1.29840.0094-0.14170.16390.4419-0.42070.6688-0.0456-0.10040.51430.3483-0.5667-0.34140.5251-0.0830.15520.5349-0.07390.8204-76.3762-42.1459-38.4256
50.73710.49650.38793.61342.36231.5020.0193-0.0274-0.11950.4448-0.18740.57390.0952-0.14850.13990.4713-0.00890.08160.15070.0250.2899-54.1565-20.4796-32.7972
62.1485-0.9439-0.23184.52251.2370.78290.23640.0435-0.0383-0.1108-0.1926-0.8026-0.21380.1625-0.04150.49720.03360.09010.20550.08080.2274-30.7149-17.6497-48.6177
73.44790.4631-0.6765.6299-0.45291.48940.1743-0.16650.1993-0.1717-0.2431-0.54770.1390.05180.04410.72420.09450.13160.05420.04270.3118-31.1363-24.3094-46.9116
88.1728-0.0616-2.6769-0.08130.08690.72490.13840.66360.11790.1660.0617-0.06870.04690.2031-0.13520.4424-0.01750.06130.3812-0.03230.3034-11.1759-45.2199-3.697
90.3358-1.0110.74832.7326-2.02191.4458-0.0944-0.0603-0.1293-0.639-0.1721-0.18510.08410.16070.09280.6873-0.0210.13210.10640.12820.1856-32.8399-20.3389-10.2789
101.68350.9128-0.2312.8486-0.95151.38540.00890.0537-0.1037-0.0738-0.14060.6351-0.001-0.16550.02960.58670.03440.08540.13010.00250.0197-52.9868-22.354810.0037
119.0024-1.37490.70080.1514-0.0889-0.00090.0478-0.83020.39260.1397-0.0416-0.298-0.52310.4581-0.07470.5377-0.066-0.07520.4898-0.0170.3626-11.7809-51.7124-38.4321
120.15110.5075-0.47014.2049-2.95441.9856-0.07990.0427-0.01380.2906-0.1217-0.49320.14480.04440.14090.44130.04-0.07110.14590.01050.2801-34.9176-71.9199-35.1925
131.5725-1.50170.32116.05910.11511.22360.14830.14180.0452-0.1536-0.11481.17630.004-0.29750.11790.6394-0.0179-0.09160.1991-0.08550.2662-60.0296-75.232-48.4836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 3669 )
2X-RAY DIFFRACTION2chain 'A' and (resid 3670 through 3830 )
3X-RAY DIFFRACTION3chain 'A' and (resid 3831 through 4069 )
4X-RAY DIFFRACTION4chain 'B' and (resid -4 through 3688 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3689 through 3830 )
6X-RAY DIFFRACTION6chain 'B' and (resid 3831 through 3973 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3974 through 4067 )
8X-RAY DIFFRACTION8chain 'C' and (resid -4 through 3704 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3705 through 3830 )
10X-RAY DIFFRACTION10chain 'C' and (resid 3831 through 4066 )
11X-RAY DIFFRACTION11chain 'D' and (resid -4 through 3686 )
12X-RAY DIFFRACTION12chain 'D' and (resid 3687 through 3854 )
13X-RAY DIFFRACTION13chain 'D' and (resid 3855 through 4066 )

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