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- PDB-6hv6: Crystal structure of PatoxP, a cysteine protease-like domain of P... -

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Basic information

Entry
Database: PDB / ID: 6hv6
TitleCrystal structure of PatoxP, a cysteine protease-like domain of Photorhabdus asymbiotica toxin PaTox
ComponentsToxin PAU_02230
KeywordsTOXIN / Cystein protease-like / PaTox toxin
Function / homology
Function and homology information


: / protein N-acetylglucosaminyltransferase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / Transferases; Glycosyltransferases; Hexosyltransferases / regulation of GTPase activity / metabolic process / toxin activity / calcium ion binding / host cell plasma membrane ...: / protein N-acetylglucosaminyltransferase activity / protein-glutamine glutaminase activity / protein-glutamine glutaminase / Transferases; Glycosyltransferases; Hexosyltransferases / regulation of GTPase activity / metabolic process / toxin activity / calcium ion binding / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Glycosyltransferase, DXD sugar-binding motif / Glycosyltransferase sugar-binding region containing DXD motif / Tox-PLDMTX domain / Dermonecrotoxin of the Papain-like fold / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesPhotorhabdus asymbiotica subsp. asymbiotica ATCC 43949 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsBogdanovic, X. / Wirth, C. / Hunte, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationCRC 746 Germany
EXC 294 BIOSS Germany
CitationJournal: J. Biol. Chem. / Year: 2019
Title: A cysteine protease-like domain enhances the cytotoxic effects of thePhotorhabdus asymbioticatoxin PaTox.
Authors: Bogdanovic, X. / Schneider, S. / Levanova, N. / Wirth, C. / Trillhaase, C. / Steinemann, M. / Hunte, C. / Aktories, K. / Jank, T.
History
DepositionOct 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jul 13, 2022Group: Advisory / Database references / Structure summary
Category: audit_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.name / _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: Toxin PAU_02230
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8938
Polymers52,2831
Non-polymers6117
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint20 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.403, 76.029, 76.324
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 Toxin PAU_02230 / Photorhabdus asymbiotica toxin / PaTox


Mass: 52282.512 Da / Num. of mol.: 1 / Mutation: C1865A
Source method: isolated from a genetically manipulated source
Details: The catalytic cysteine 1865 was mutated to alanine
Source: (gene. exp.) Photorhabdus asymbiotica subsp. asymbiotica ATCC 43949 (bacteria)
Gene: PAU_02230 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C7BKP9, Transferases; Glycosyltransferases; Hexosyltransferases, protein-glutamine glutaminase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 25.7% w/v Polyethylene glycol 8000, 150 mM HEPES pH 7.5, 60 mM potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2037 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2037 Å / Relative weight: 1
ReflectionResolution: 2→53.9 Å / Num. obs: 25589 / % possible obs: 100 % / Redundancy: 95.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.261 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 62 % / Rmerge(I) obs: 2.298 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1856 / CC1/2: 0.772 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.001→53.864 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.82
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 690 2.75 %RANDOM SELECTION
Rwork0.1748 ---
obs0.1758 25108 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.001→53.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 39 184 2555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062423
X-RAY DIFFRACTIONf_angle_d0.7383250
X-RAY DIFFRACTIONf_dihedral_angle_d10.0941495
X-RAY DIFFRACTIONf_chiral_restr0.048345
X-RAY DIFFRACTIONf_plane_restr0.005414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0008-2.15530.23251290.20614483X-RAY DIFFRACTION92
2.1553-2.37220.221610.18384838X-RAY DIFFRACTION100
2.3722-2.71540.19391470.17744930X-RAY DIFFRACTION100
2.7154-3.42110.25311140.18364986X-RAY DIFFRACTION100
3.4211-53.8840.20091390.16315181X-RAY DIFFRACTION100
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)
15.53031.4114-1.80492.4147-0.15280.63550.3426-0.7731-1.48740.3462-0.2188-0.1940.6940.4361-0.22480.48770.1243-0.03650.42710.08980.451127.484319.067459.0644
23.8717-0.48010.16924.58710.23254.1519-0.2526-0.0360.72990.12920.2014-0.1103-0.33840.02070.02440.23660.0606-0.09370.2325-0.00950.330843.574331.180944.3825
34.2945-2.4689-5.21552.90992.09396.9088-0.08560.0399-0.25070.2072-0.1653-0.25740.1056-0.16030.24860.22580.0366-0.03450.3272-0.02570.304825.599926.472958.6786
44.52490.5681-0.3155.1329-1.84133.7683-0.0083-0.2618-0.0169-0.05590.0275-0.1314-0.01620.3664-0.00090.2623-0.0580.01690.2279-0.09450.236215.299729.574856.7129
53.0189-0.508-0.71363.40321.32443.619-0.03740.02680.3568-0.42680.0210.2609-0.3906-0.02320.04110.2599-0.0145-0.07590.1701-0.0390.23617.731532.796148.8029
62.3962-0.37280.05563.92840.82443.6779-0.179-0.60570.38960.4323-0.07480.6893-0.0551-0.33650.15260.26990.00010.03750.3871-0.16890.37345.975837.853763.7511
74.190.99630.59173.47770.37652.839-0.16890.40250.3112-0.38650.13310.8151-0.0405-0.20620.06270.3554-0.0041-0.15710.27320.02810.42832.840238.462349.5959
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1730 through 1745 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1746 through 1820 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1821 through 1842 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1843 through 1864 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1865 through 1932 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1933 through 2000 )
7X-RAY DIFFRACTION7chain 'A' and (resid 2001 through 2032 )

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