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- PDB-7rws: Structure of SAVED domain of Cap5 from Lactococcus lactis in comp... -

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Basic information

Entry
Database: PDB / ID: 7rws
TitleStructure of SAVED domain of Cap5 from Lactococcus lactis in complex with cGAMP
ComponentsSAVED domain-containing protein
KeywordsUNKNOWN FUNCTION / SAVED Sensor cGAMP Second messenger
Function / homologyHNH endonuclease / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / HNH nuclease / metal ion binding / 3'2'-cGAMP / SMODS-associated and fused to various effectors domain-containing protein
Function and homology information
Biological speciesLactococcus lactis subsp. cremoris IBB477 (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuang, R.H. / Chakravarti, A. / Fatma, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2021
Title: Molecular mechanisms of the CdnG-Cap5 antiphage defense system employing 3',2'-cGAMP as the second messenger.
Authors: Fatma, S. / Chakravarti, A. / Zeng, X. / Huang, R.H.
History
DepositionAug 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2882
Polymers30,6141
Non-polymers6741
Water5,999333
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)68.696, 126.713, 83.439
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SAVED domain-containing protein


Mass: 30613.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris IBB477 (lactic acid bacteria)
Gene: AJ89_14580 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E7G0A2
#2: Chemical ChemComp-4UR / 3'2'-cGAMP / 2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one


Mass: 674.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10-12.5% PEG6000, 100 mM Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 34016 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 3297 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RWK

7rwk


Resolution: 1.8→33.04 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 1995 5.86 %
Rwork0.1667 32021 -
obs0.1681 34016 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.93 Å2 / Biso mean: 21.8442 Å2 / Biso min: 6 Å2
Refinement stepCycle: final / Resolution: 1.8→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 45 333 2450
Biso mean--15.35 33.52 -
Num. residues----255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.2321430.17352121226493
1.84-1.890.18941310.16642244237598
1.89-1.950.21711470.17292252239999
1.95-2.010.21421290.15742291242099
2.01-2.080.18321530.16482271242499
2.08-2.160.19041430.166722682411100
2.16-2.260.19281460.15922852431100
2.26-2.380.21521310.16752286241799
2.38-2.530.1941410.174723072448100
2.53-2.730.20831510.177222942445100
2.73-30.22081430.177823172460100
3-3.430.17231400.161923352475100
3.43-4.320.15911450.152123432488100
4.33-33.040.18521520.17422407255998

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