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- PDB-9l5u: Papain-like cysteine protease toxin/immunity pair -

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Basic information

Entry
Database: PDB / ID: 9l5u
TitlePapain-like cysteine protease toxin/immunity pair
Components
  • Cpi1
  • DUF4150 domain-containing protein
KeywordsTOXIN / Papain-like cysteine protease / toxin/immunity pair
Function / homology
Function and homology information


peptidase activity / proteolysis / ATP binding / membrane
Similarity search - Function
Tox-PAAR-like domain / Toxin PAAR-like domain / Peptidase C39 family / Peptidase C39, bacteriocin processing
Similarity search - Domain/homology
DUF4150 domain-containing protein / Aec11
Similarity search - Component
Biological speciesEscherichia coli DSM 30083 = JCM 1649 = ATCC 11775 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å
AuthorsChen, P.-P. / Hsia, K.-C. / Ting, S.-Y. / Chen, Y.-C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Plos Biol. / Year: 2025
Title: An interbacterial cysteine protease toxin inhibits cell growth by targeting type II DNA topoisomerases GyrB and ParE.
Authors: Song, P.Y. / Tsai, C.E. / Chen, Y.C. / Huang, Y.W. / Chen, P.P. / Wang, T.H. / Hu, C.Y. / Chen, P.Y. / Ku, C. / Hsia, K.C. / Ting, S.Y.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF4150 domain-containing protein
B: DUF4150 domain-containing protein
C: Cpi1
D: Cpi1


Theoretical massNumber of molelcules
Total (without water)56,1124
Polymers56,1124
Non-polymers00
Water5,405300
1
A: DUF4150 domain-containing protein
C: Cpi1


Theoretical massNumber of molelcules
Total (without water)28,0562
Polymers28,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-11 kcal/mol
Surface area11160 Å2
MethodPISA
2
B: DUF4150 domain-containing protein
D: Cpi1


Theoretical massNumber of molelcules
Total (without water)28,0562
Polymers28,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-10 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.137, 104.137, 128.709
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-252-

HOH

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Components

#1: Protein DUF4150 domain-containing protein / Filamentous hemagglutinin family outer membrane protein


Mass: 17271.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cpe1
Source: (gene. exp.) Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 (bacteria)
Gene: xmtU, D3C88_22085, IFC14_004794, NCTC9001_00711 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2QG14
#2: Protein Cpi1 / Aec11


Mass: 10784.638 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DSM 30083 = JCM 1649 = ATCC 11775 (bacteria)
Gene: aec11, xmtV, B6R31_003793, BK383_27470, BvCmsNSP007_02591, D3C88_22090, IFC14_004793, NCTC9001_00710
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6TKV7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: magnesium formate, sodium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 29, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.87→29.49 Å / Num. obs: 85800 / % possible obs: 98.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 31.03 Å2 / CC1/2: 1 / Net I/σ(I): 28.9
Reflection shellResolution: 1.87→1.94 Å / Num. unique obs: 5359 / CC1/2: 0.935

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000v7.22data reduction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MAD / Resolution: 1.87→29.49 Å / SU ML: 0.1574 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1971 2963 3.45 %
Rwork0.1713 82837 -
obs0.1722 85800 77.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.03 Å2
Refinement stepCycle: LAST / Resolution: 1.87→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 0 300 3888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00843662
X-RAY DIFFRACTIONf_angle_d0.96794958
X-RAY DIFFRACTIONf_chiral_restr0.061558
X-RAY DIFFRACTIONf_plane_restr0.0052620
X-RAY DIFFRACTIONf_dihedral_angle_d5.7529483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.2536830.26512329X-RAY DIFFRACTION45.27
1.9-1.940.2951920.23962581X-RAY DIFFRACTION50.49
1.94-1.970.234950.21982675X-RAY DIFFRACTION51.86
1.97-2.010.2446940.20692667X-RAY DIFFRACTION52.38
2.01-2.050.1851970.19942714X-RAY DIFFRACTION53.15
2.05-2.090.2219980.20262792X-RAY DIFFRACTION54.45
2.09-2.140.19151070.19332916X-RAY DIFFRACTION56.93
2.14-2.20.21111080.18243089X-RAY DIFFRACTION60.11
2.2-2.260.18041150.183242X-RAY DIFFRACTION63.64
2.26-2.320.18341280.16273542X-RAY DIFFRACTION69.23
2.32-2.40.19011520.16694033X-RAY DIFFRACTION78.69
2.4-2.480.21561680.16764702X-RAY DIFFRACTION91.92
2.48-2.580.22381760.17875096X-RAY DIFFRACTION99.38
2.58-2.70.17911830.185103X-RAY DIFFRACTION99.96
2.7-2.840.21471790.18125107X-RAY DIFFRACTION99.98
2.84-3.020.20531850.185140X-RAY DIFFRACTION99.96
3.02-3.250.18331860.18115126X-RAY DIFFRACTION99.94
3.25-3.580.21181820.16815101X-RAY DIFFRACTION99.83
3.58-4.10.18221840.14825077X-RAY DIFFRACTION99.47
4.1-5.160.1471830.13155040X-RAY DIFFRACTION98.53
5.16-29.490.22971680.18244765X-RAY DIFFRACTION92.88
Refinement TLS params.Method: refined / Origin x: 8.75761908752 Å / Origin y: 18.3110427141 Å / Origin z: 12.1093853548 Å
111213212223313233
T0.1151291757 Å2-0.0242983236816 Å20.017051385757 Å2-0.164879710727 Å20.0201900567198 Å2--0.125646910973 Å2
L0.54077243905 °2-0.373294037209 °2-0.401103385242 °2-1.26066226309 °20.613247850818 °2--1.22424108915 °2
S-0.0965600455655 Å °-0.03630011493 Å °-0.102266120551 Å °0.271993671572 Å °0.0768400555686 Å °0.0913915365752 Å °0.203084069815 Å °-0.0168791461899 Å °-0.00805392343686 Å °
Refinement TLS groupSelection details: all

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