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- PDB-7t5t: Structure of Thauera sp. K11 CapP -

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Basic information

Entry
Database: PDB / ID: 7t5t
TitleStructure of Thauera sp. K11 CapP
ComponentsCapP toxin
KeywordsHYDROLASE / Zinc metallopeptidase / IrrE / cysteine switch
Function / homology: / IrrE N-terminal-like domain / IrrE N-terminal-like domain / metal ion binding / Toxin
Function and homology information
Biological speciesThauera sp. K11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsLau, R.K. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI148814 United States
CitationJournal: Embo J. / Year: 2022
Title: A conserved signaling pathway activates bacterial CBASS immune signaling in response to DNA damage.
Authors: Lau, R.K. / Enustun, E. / Gu, Y. / Nguyen, J.V. / Corbett, K.D.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CapP toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3996
Polymers32,7271
Non-polymers6725
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.309, 95.309, 104.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

21A-666-

HOH

31A-692-

HOH

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Components

#1: Protein CapP toxin


Mass: 32727.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thauera sp. K11 (bacteria) / Gene: CCZ27_23105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A290ZVI6
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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, hanging drop / Details: 0.1 M CHES pH 9.5, 1.8 M LiSO4, 0.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.35→39.49 Å / Num. obs: 106052 / % possible obs: 99.8 % / Redundancy: 13.1 % / Biso Wilson estimate: 22.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.016 / Net I/σ(I): 18.7
Reflection shellResolution: 1.35→1.37 Å / Rmerge(I) obs: 2.884 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5070 / CC1/2: 0.443 / Rpim(I) all: 0.853

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→39.49 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.9543
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1679 2905 2.74 %
Rwork0.1621 102934 -
obs0.1622 105839 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.51 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 37 343 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752300
X-RAY DIFFRACTIONf_angle_d0.9443140
X-RAY DIFFRACTIONf_chiral_restr0.0759338
X-RAY DIFFRACTIONf_plane_restr0.0081401
X-RAY DIFFRACTIONf_dihedral_angle_d15.3653819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.43921180.42684641X-RAY DIFFRACTION95.72
1.37-1.390.33491450.35454795X-RAY DIFFRACTION99.22
1.39-1.420.34311490.31354826X-RAY DIFFRACTION99.16
1.42-1.450.31981450.27594841X-RAY DIFFRACTION99.66
1.45-1.480.26931360.23814810X-RAY DIFFRACTION99.48
1.48-1.510.2141390.18864871X-RAY DIFFRACTION99.7
1.51-1.540.1991460.17444841X-RAY DIFFRACTION99.72
1.54-1.580.18451310.17444876X-RAY DIFFRACTION99.9
1.58-1.630.19011420.16854873X-RAY DIFFRACTION99.84
1.63-1.670.2221310.17654883X-RAY DIFFRACTION99.88
1.67-1.730.16891330.16054877X-RAY DIFFRACTION99.82
1.73-1.790.17311370.14184890X-RAY DIFFRACTION99.98
1.79-1.860.17291370.14254894X-RAY DIFFRACTION99.98
1.86-1.950.15261310.14184939X-RAY DIFFRACTION99.94
1.95-2.050.18481430.14934890X-RAY DIFFRACTION99.98
2.05-2.180.15441370.14934947X-RAY DIFFRACTION99.94
2.18-2.340.15841350.14264934X-RAY DIFFRACTION100
2.34-2.580.16241420.14534982X-RAY DIFFRACTION100
2.58-2.950.1551300.15454996X-RAY DIFFRACTION100
2.95-3.720.14951490.15875048X-RAY DIFFRACTION99.88
3.72-39.490.15851490.16495280X-RAY DIFFRACTION99.76

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