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- PDB-8fm1: Structure of CBASS Cap5 from Pseudomonas syringae in the absence ... -

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Basic information

Entry
Database: PDB / ID: 8fm1
TitleStructure of CBASS Cap5 from Pseudomonas syringae in the absence of a ligand (apo form dimer)
ComponentsSAVED domain-containing protein
KeywordsIMMUNE SYSTEM / cyclic dinucleotide / bacterial immunity / CBASS / Cap5 effector DNA endonuclease / viral defense
Function / homologyHNH endonuclease / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / HNH nuclease / metal ion binding / HNH endonuclease
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsRechkoblit, O. / Kreitler, D.F. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM13170 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides.
Authors: Rechkoblit, O. / Sciaky, D. / Kreitler, D.F. / Buku, A. / Kottur, J. / Aggarwal, A.K.
History
DepositionDec 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAVED domain-containing protein
B: SAVED domain-containing protein
C: SAVED domain-containing protein
D: SAVED domain-containing protein
E: SAVED domain-containing protein
F: SAVED domain-containing protein
G: SAVED domain-containing protein
H: SAVED domain-containing protein
I: SAVED domain-containing protein
J: SAVED domain-containing protein
K: SAVED domain-containing protein
L: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,01624
Polymers513,23112
Non-polymers78512
Water00
1
A: SAVED domain-containing protein
B: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6694
Polymers85,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SAVED domain-containing protein
D: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6694
Polymers85,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: SAVED domain-containing protein
F: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6694
Polymers85,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: SAVED domain-containing protein
H: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6694
Polymers85,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: SAVED domain-containing protein
J: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6694
Polymers85,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: SAVED domain-containing protein
L: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6694
Polymers85,5382
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.428, 159.428, 433.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 16 through 59 or resid 81...
d_2ens_1(chain "B" and (resid 16 through 59 or resid 81...
d_3ens_1(chain "C" and (resid 16 through 59 or resid 81...
d_4ens_1(chain "D" and (resid 16 through 59 or resid 81...
d_5ens_1(chain "E" and (resid 16 through 59 or resid 81...
d_6ens_1(chain "F" and (resid 16 through 59 or resid 81...
d_7ens_1(chain "G" and (resid 16 through 59 or resid 81...
d_8ens_1(chain "H" and (resid 16 through 59 or resid 81...
d_9ens_1(chain "I" and (resid 16 through 59 or resid 81...
d_10ens_1(chain "J" and (resid 16 through 59 or resid 81...
d_11ens_1(chain "K" and (resid 16 through 59 or resid 81...
d_12ens_1(chain "L" and (resid 16 through 59 or resid 81...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRPROA3 - 46
d_12ens_1ALALEUA51 - 350
d_21ens_1THRPROB6 - 49
d_22ens_1ALALEUB57 - 356
d_31ens_1THRPROC2 - 45
d_32ens_1ALALEUC50 - 349
d_41ens_1THRPROD3 - 46
d_42ens_1ALALEUD51 - 350
d_51ens_1THRPROE3 - 46
d_52ens_1ALALEUE51 - 350
d_61ens_1THRPROF1 - 44
d_62ens_1ALALEUF52 - 351
d_71ens_1THRPROG3 - 46
d_72ens_1ALALEUG52 - 351
d_81ens_1THRPROH1 - 44
d_82ens_1ALALEUH53 - 352
d_91ens_1THRPROI3 - 46
d_92ens_1ALALEUI48 - 347
d_101ens_1THRPROJ2 - 45
d_102ens_1ALALEUJ48 - 347
d_111ens_1THRPROK3 - 46
d_112ens_1ALALEUK59 - 358
d_121ens_1THRPROL1 - 44
d_122ens_1ALALEUL54 - 353

NCS oper:
IDCodeMatrixVector
1given(-0.701112835297, -0.707216480417, -0.0910255019719), (-0.706908570704, 0.672668206882, 0.218626979384), (-0.0933866416924, 0.217628888885, -0.971553705091)-215.515641014, -73.9332118748, -128.047270151
2given(0.646610506973, -0.589598412234, 0.484012979748), (-0.756922853496, -0.417167384003, 0.50302998676), (-0.0946712529147, -0.691624960521, -0.716025326267)4.34171266095, -47.2505460803, -130.382565287
3given(-0.0791645496243, -0.71371809539, -0.695945008169), (0.746101495879, 0.420575881866, -0.516186483201), (0.661109319198, -0.560109282109, 0.499211438336)-154.244247968, 79.6590276633, 34.3967866515
4given(0.334787320467, 0.942162737654, -0.0157106916139), (0.267649527271, -0.0790938186667, 0.960264493981), (0.903482805927, -0.325689336063, -0.278649018963)-8.26244950302, 17.643237526, -6.85637487775
5given(-0.910873677383, 0.366651537397, 0.189409065189), (-0.204160154811, -0.00148557270601, -0.97893637396), (-0.358647145589, -0.930357158944, 0.0762088037103)-150.276609851, -154.898405281, -142.125012697
6given(-0.712594573999, -0.61607550617, 0.335648542087), (0.631881035664, -0.355702462744, 0.688623347532), (-0.304852964354, 0.702799209373, 0.642758073796)-148.585332294, 93.5560914911, 25.4371784291
7given(0.89968641903, 0.197501842666, -0.38930369836), (-0.236998308793, -0.527941797574, -0.81554231037), (-0.366600803385, 0.825996658902, -0.42817446262)8.46373041629, -103.043930813, -45.2780607478
8given(-0.515786386042, 0.148606375278, -0.843730140033), (0.561844968121, 0.802155145086, -0.202181490275), (0.646757014474, -0.578327993823, -0.497234447509)-123.293149084, 67.2120753095, -58.6859153209
9given(0.349082804419, 0.266199073501, 0.898487200202), (-0.935842612392, 0.0495393011002, 0.348918991282), (0.0483714842607, -0.962644228629, 0.266413754519)86.2600639367, -86.4521476266, -87.9191439694
10given(-0.163006536333, 0.837551386457, 0.521475353354), (0.811726522604, -0.186594349903, 0.553428045084), (0.560828781014, 0.513507763941, -0.649446575754)-0.26753632398, 82.6317408376, -87.466662426
11given(-0.569915286085, 0.778903078477, -0.261737580461), (-0.49376740187, -0.579235374444, -0.648598592231), (-0.656803105609, -0.24040876717, 0.714712043505)-96.0828026173, -149.540917267, -159.070813149

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Components

#1: Protein
SAVED domain-containing protein / CBASS Cap5


Mass: 42769.238 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P0QGK5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
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

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.21 % / Description: rectangular bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1 M trisodium citrate, 0.1 M Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Nov 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.16→112.733 Å / Num. obs: 85862 / % possible obs: 95.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 129.47 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.8
Reflection shellResolution: 3.16→3.337 Å / Num. unique obs: 4294 / CC1/2: 0.541 / % possible all: 51.1

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Processing

Software
NameVersionClassification
PHENIX1.18rc7_3834refinement
PHENIX1.18rc7_3834refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.16→112.73 Å / SU ML: 0.4335 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.5183
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2935 2000 2.33 %
Rwork0.2397 83838 -
obs0.2409 85838 89.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.57 Å2
Refinement stepCycle: LAST / Resolution: 3.16→112.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32950 0 12 0 32962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006233718
X-RAY DIFFRACTIONf_angle_d1.047945929
X-RAY DIFFRACTIONf_chiral_restr0.06135145
X-RAY DIFFRACTIONf_plane_restr0.00616106
X-RAY DIFFRACTIONf_dihedral_angle_d29.89512490
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.25872048205
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS2.29596094839
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.98585707163
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS1.84921493356
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS2.01348233096
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS1.74580168646
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS2.23018873014
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS2.08854685701
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS2.09450104543
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS1.99273410193
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS2.56850259136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.16-3.240.3777200.3479832X-RAY DIFFRACTION12.58
3.24-3.330.4005710.34392984X-RAY DIFFRACTION45.05
3.33-3.430.37781380.33095774X-RAY DIFFRACTION87.29
3.43-3.540.36081580.3246633X-RAY DIFFRACTION99.96
3.54-3.660.37851580.31546618X-RAY DIFFRACTION99.99
3.66-3.810.36881590.29246656X-RAY DIFFRACTION99.93
3.81-3.980.35191590.29196674X-RAY DIFFRACTION99.97
3.98-4.190.3211590.27176689X-RAY DIFFRACTION100
4.19-4.460.31221600.25346684X-RAY DIFFRACTION100
4.46-4.80.28481600.23536724X-RAY DIFFRACTION99.97
4.8-5.280.27211600.23156729X-RAY DIFFRACTION99.91
5.28-6.050.3161620.25566797X-RAY DIFFRACTION99.96
6.05-7.620.30931640.24536867X-RAY DIFFRACTION99.99
7.62-112.730.23081720.18177177X-RAY DIFFRACTION99.53

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