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- PDB-8ysq: Crystal structure of SAVED domain of Cap5 from Deinococcus wulumu... -

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Basic information

Entry
Database: PDB / ID: 8ysq
TitleCrystal structure of SAVED domain of Cap5 from Deinococcus wulumuqiensis
ComponentsSAVED domain-containing protein
KeywordsIMMUNE SYSTEM / CD-NTase-associated protein 5 / SAVED
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / SAVED domain-containing protein
Function and homology information
Biological speciesDeinococcus wulumuqiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-039-001-MY3 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural insights into signaling promiscuity of the CBASS anti-phage defense system from a radiation-resistant bacterium.
Authors: Yang, C.S. / Shie, M.Y. / Huang, S.W. / Wang, Y.C. / Hou, M.H. / Chen, C.J. / Chen, Y.
History
DepositionMar 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 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: SAVED domain-containing protein


Theoretical massNumber of molelcules
Total (without water)45,3111
Polymers45,3111
Non-polymers00
Water5,477304
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)37.468, 43.126, 45.047
Angle α, β, γ (deg.)77.745, 67.352, 74.926
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein SAVED domain-containing protein / CD-NTase-associated protein 5


Mass: 45310.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus wulumuqiensis (bacteria) / Gene: DVJ83_15715 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A345ILN8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 1.42 Å3/Da / Density % sol: 13.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 6.5, 28 % w/v PEG 2000 MME.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. obs: 23396 / % possible obs: 96.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 16.66 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.044 / Net I/σ(I): 31.206
Reflection shellResolution: 1.76→1.83 Å / Num. unique obs: 2347 / CC1/2: 0.992

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→23.98 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 23.1064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 730 5 %
Rwork0.18 22202 -
obs0.1823 23371 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.12 Å2
Refinement stepCycle: LAST / Resolution: 1.76→23.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 0 304 2354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462107
X-RAY DIFFRACTIONf_angle_d0.78462864
X-RAY DIFFRACTIONf_chiral_restr0.0499326
X-RAY DIFFRACTIONf_plane_restr0.0071371
X-RAY DIFFRACTIONf_dihedral_angle_d12.3671801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.840.33671370.21572589X-RAY DIFFRACTION88.56
1.84-1.940.27811490.21322850X-RAY DIFFRACTION98.07
1.94-2.060.25711510.18982868X-RAY DIFFRACTION98.05
2.06-2.220.20941520.17892874X-RAY DIFFRACTION98.09
2.22-2.440.23581490.18262842X-RAY DIFFRACTION97.33
2.44-2.80.25581460.18842782X-RAY DIFFRACTION95.75
2.8-3.520.23651430.17612711X-RAY DIFFRACTION92.57
3.52-23.980.17151420.16072686X-RAY DIFFRACTION92.15
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)
10.48856590170.5426479570810.1050410170871.064706596520.345414523810.864282203526-0.4395013725310.08266461266640.167981616917-0.807175637211-0.02602960254160.184601082627-0.2018878471410.249590316595-0.4392803558940.0228421570954-0.01785283994970.0884631119780.1989015436090.04393931568490.05398644264795.284103763798.29042394101-9.11851957903
20.09322660628170.07123471858410.05297417133730.8568700472790.1961014694060.286644106653-0.2628044276360.1915903758960.18614072284-0.9558786737710.137652231394-0.345135749906-0.2742070318870.17989893470.05740050791640.191568001707-0.0493197376121-0.026835931340.2598774690410.04244328566650.1028130520384.0699850158411.2957790387-10.4096196761
30.05703114562830.0287714631160.03283574371570.08876075097620.03550742020590.0159845238282-0.0719448360424-0.04735640108910.04536033390770.03746405582390.0220198123601-0.0678748717362-0.1089711691350.0679955912616-0.04366471268130.0883724079183-0.00719050733186-0.01262096167170.1371188542670.00467342232880.1527788494157.5407881155310.09705544955.55163070825
40.1568839770860.14196584039-0.06336684079520.0940453559398-0.0316737417290.483795665517-0.0832434711512-0.02650301077620.194980369216-0.104150186548-0.08940663229340.150449878984-0.08274111588130.107510354145-0.2646322649330.116964424181-0.00290425932036-0.04952854573630.0955297001345-0.01176428428430.196112687483-2.8133889271611.6159738822-1.66482348016
50.03073120542370.0391749781380.01667606073610.623779043245-0.1990018745710.0880799462117-0.1157672472010.02062570764910.214908648987-0.65194212908-0.002092389299540.1905027316360.253473341508-0.011863195708-0.05971059607750.160479710648-0.00632167092463-0.04110827465110.126180156745-0.01401523543430.12133330705-2.800369233481.87867297322-9.95779301326
60.393159412350.0737867083596-0.005090611882760.1956205974790.08944853496820.208280129351-0.00358766994131-0.171521403827-0.307423956015-0.139226336980.03115586102790.5887842704590.1416318719980.14968195968-0.02956654932980.270269184066-0.0296139348739-0.04538690523950.0671214681206-0.03364952456760.0264881120099-7.03306867048-12.6728378288-2.24115257903
70.3053115592820.413332871496-0.001242731556020.9900451099120.09950175616720.2384187696210.00756636165923-0.0806482503485-0.0684031063926-0.0555831295397-0.00396678231570.1834132624860.08940854937760.00887408049562-0.005979051395160.09804259735910.0187011771278-0.004801202588760.09576112372810.0008782021427270.0863772629966-4.17375092488-11.90053683052.81077433894
80.07690638903880.01160189289150.03581252698320.2259549460730.04081515339650.1893992338110.00680488827241-0.0864940805231-0.0757902876104-0.0189547753492-0.01030595118370.3871178812210.1269847111670.119320769531-0.02165580303470.115617349399-0.002605205854760.05497909796490.0946439721970.01386132648370.116471642206-3.98125318853-5.451773970237.93390991325
90.04314748494330.1057629786090.01990431738490.368533859193-0.2502519038390.361572548495-0.02395036072280.0697370611506-0.1813796470690.789762428075-0.4988007223160.0522223600491-0.2803210475150.437253120338-0.2019421215840.08260750087320.01578155291540.06437557493250.122040606277-0.07507383679340.1153030904182.93639296212-3.3858529357910.8435952865
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 141 through 161 )141 - 1611 - 21
22chain 'A' and (resid 162 through 192 )162 - 19222 - 52
33chain 'A' and (resid 193 through 211 )193 - 21153 - 71
44chain 'A' and (resid 212 through 241 )212 - 24172 - 101
55chain 'A' and (resid 242 through 259 )242 - 259102 - 119
66chain 'A' and (resid 260 through 287 )260 - 287120 - 147
77chain 'A' and (resid 288 through 350 )288 - 350148 - 210
88chain 'A' and (resid 351 through 374 )351 - 374211 - 234
99chain 'A' and (resid 375 through 401 )375 - 401235 - 261

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