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- PDB-6vm5: Structure of Moraxella osloensis Cap4 SAVED/CARF-domain containin... -

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Basic information

Entry
Database: PDB / ID: 6vm5
TitleStructure of Moraxella osloensis Cap4 SAVED/CARF-domain containing receptor
ComponentsSAVED domain-containing protein
KeywordsHYDROLASE / nuclease / DUF4297 / SAVED / CARF / phage immunity
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / Hydrolases; Acting on ester bonds / CD-NTase-associated protein 4
Function and homology information
Biological speciesMoraxella osloensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsLowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Antine, S.P. / Cabrera, V. / Schwede, F. / Mekalanos, J.J. / Shao, S. / Lee, A.S.Y. / Kranzusch, P.J.
CitationJournal: Cell / Year: 2020
Title: CBASS Immunity Uses CARF-Related Effectors to Sense 3'-5'- and 2'-5'-Linked Cyclic Oligonucleotide Signals and Protect Bacteria from Phage Infection.
Authors: Lowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Mathews, I.T. / Antine, S.P. / Cabrera, V.J. / Kashin, D. / Niemann, P. / Jain, M. / Schwede, F. / Mekalanos, J.J. / Shao, S. ...Authors: Lowey, B. / Whiteley, A.T. / Keszei, A.F.A. / Morehouse, B.R. / Mathews, I.T. / Antine, S.P. / Cabrera, V.J. / Kashin, D. / Niemann, P. / Jain, M. / Schwede, F. / Mekalanos, J.J. / Shao, S. / Lee, A.S.Y. / Kranzusch, P.J.
History
DepositionJan 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6382
Polymers52,6141
Non-polymers241
Water1,20767
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)157.593, 157.593, 63.318
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein SAVED domain-containing protein / Cap4


Mass: 52614.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella osloensis (bacteria) / Gene: FEF33_11620, MOTT16_09860 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K8K5C5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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

CrystalDensity Matthews: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 110 mM Tris-HCl pH 8.5, 21% PEG-400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99998 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.34→49.36 Å / Num. obs: 37860 / % possible obs: 99.2 % / Redundancy: 11.2 % / Biso Wilson estimate: 59.42 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 15.3
Reflection shellResolution: 2.34→2.43 Å / Redundancy: 10.6 % / Num. unique obs: 3455 / CC1/2: 0.413 / Rpim(I) all: 0.895 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished Se-Met version of the same protein determied by SAD phasing

Resolution: 2.35→49.36 Å / SU ML: 0.4081 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3605
RfactorNum. reflection% reflection
Rfree0.2336 2004 5.31 %
Rwork0.2066 --
obs0.208 37711 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.51 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 1 67 3453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573454
X-RAY DIFFRACTIONf_angle_d0.71014657
X-RAY DIFFRACTIONf_chiral_restr0.0474514
X-RAY DIFFRACTIONf_plane_restr0.0045600
X-RAY DIFFRACTIONf_dihedral_angle_d6.30622069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.43731390.36472413X-RAY DIFFRACTION96.27
2.41-2.470.36731380.33932518X-RAY DIFFRACTION99.7
2.47-2.550.34771360.31022560X-RAY DIFFRACTION99.67
2.55-2.630.3371420.28092524X-RAY DIFFRACTION99.85
2.63-2.720.26531470.26272543X-RAY DIFFRACTION99.96
2.72-2.830.28721380.25032539X-RAY DIFFRACTION99.93
2.83-2.960.30871450.25222530X-RAY DIFFRACTION100
2.96-3.120.28081470.242555X-RAY DIFFRACTION100
3.12-3.310.24171450.22062559X-RAY DIFFRACTION100
3.31-3.570.22211420.21052552X-RAY DIFFRACTION100
3.57-3.930.21941430.19362577X-RAY DIFFRACTION100
3.93-4.490.19771420.16972583X-RAY DIFFRACTION100
4.49-5.660.20791440.16782592X-RAY DIFFRACTION100
5.66-49.360.20341560.19122662X-RAY DIFFRACTION99.79
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)
12.17812937677-1.01388968041-0.6503075072760.8032990204-0.602907372231.35616460826-0.00028385485049-0.421583734875-1.05860252485-0.7073597135150.0243814940534-0.3873278886511.25301997564-0.459726977577-0.01862270919411.14830986784-0.35830093437-0.004768357667050.8879019084930.04192408152730.682639191392-55.475147202516.5010134858-19.5270729595
21.51578775699-0.315606074976-0.4071351153181.76877522153-0.7175418864691.21260713581-0.281703448850.0649650586854-0.390594415734-0.4513365311360.3442216062690.2917228644370.2126974952240.224338185007-0.05929655983320.905814037199-0.331082692435-0.04419179626670.5011278464920.05368061468780.475796331579-63.927522520418.2696043172-23.3089949296
32.37429227095-0.7776574665290.7819127043191.426843225710.846724380131.01104297302-0.0514701681076-0.20399005309-0.000868354718254-0.103089157288-0.00480808772089-0.0958263878348-0.0261367625775-0.2671168445530.2198191077130.454178331514-0.181104111106-0.07519432766370.454980684569-0.02340769914560.364899441147-52.890936354665.2133874517-21.3199618968
41.813969660570.8396455630481.813758477352.66301897711-0.3202656776642.45152603521-0.333675595754-0.9109622292980.2262569628750.818166021880.04131493923860.276481886363-0.168669946463-0.9268211577530.1183613667710.553152042421-0.1050906404940.06187093495920.749855565157-0.09558803434140.357121393217-53.766168129164.5764002165-11.7972581376
50.4774632715170.972499425910.5236647559561.39914979121-0.3870934213030.282997754447-0.02676801890340.0107372004182-0.0460401405692-0.3318638926250.149502396113-0.1180064098660.2897777520630.005244762453880.2292444775470.664486016467-0.2642782875080.00363504213610.468884062037-0.08862516437150.534558974737-50.39666199542.0001324453-24.0443729131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 321 through 356 )
2X-RAY DIFFRACTION2chain 'A' and (resid 357 through 463 )
3X-RAY DIFFRACTION3chain 'A' and (resid 15 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 191 )
5X-RAY DIFFRACTION5chain 'A' and (resid 192 through 320 )

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