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- PDB-7rwm: Structure of Cap5 from Lactococcus lactis -

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Basic information

Entry
Database: PDB / ID: 7rwm
TitleStructure of Cap5 from Lactococcus lactis
ComponentsSAVED domain-containing protein
KeywordsUNKNOWN FUNCTION / DNA nuclease SAVED Sensor Effector
Function / homologyHNH endonuclease / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / HNH nuclease / endonuclease activity / metal ion binding / 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: 3.4 Å
AuthorsHuang, R.H. / Fatma, S. / Chakravarti, A.
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
B: SAVED domain-containing protein
C: SAVED domain-containing protein
D: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,6888
Polymers178,4264
Non-polymers2624
Water00
1
A: SAVED domain-containing protein
B: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3444
Polymers89,2132
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-23 kcal/mol
Surface area33310 Å2
MethodPISA
2
C: SAVED domain-containing protein
D: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3444
Polymers89,2132
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-21 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.772, 180.772, 93.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 through 47 or resid 49...
21(chain B and (resid 16 through 47 or resid 49...
31(chain C and (resid 16 through 47 or resid 49...
41(chain D and (resid 16 through 47 or resid 49...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 16 through 47 or resid 49...A16 - 47
121(chain A and (resid 16 through 47 or resid 49...A49
131(chain A and (resid 16 through 47 or resid 49...A51 - 60
141(chain A and (resid 16 through 47 or resid 49...A71 - 74
151(chain A and (resid 16 through 47 or resid 49...A76 - 108
161(chain A and (resid 16 through 47 or resid 49...A110 - 383
211(chain B and (resid 16 through 47 or resid 49...B16 - 47
221(chain B and (resid 16 through 47 or resid 49...B49
231(chain B and (resid 16 through 47 or resid 49...B51 - 60
241(chain B and (resid 16 through 47 or resid 49...B71 - 74
251(chain B and (resid 16 through 47 or resid 49...B76
261(chain B and (resid 16 through 47 or resid 49...B226 - 383
311(chain C and (resid 16 through 47 or resid 49...C16 - 47
321(chain C and (resid 16 through 47 or resid 49...C49
331(chain C and (resid 16 through 47 or resid 49...C51 - 60
341(chain C and (resid 16 through 47 or resid 49...C0
351(chain C and (resid 16 through 47 or resid 49...C8
361(chain C and (resid 16 through 47 or resid 49...C226 - 283
371(chain C and (resid 16 through 47 or resid 49...C16 - 383
381(chain C and (resid 16 through 47 or resid 49...C291 - 383
411(chain D and (resid 16 through 47 or resid 49...D16 - 47
421(chain D and (resid 16 through 47 or resid 49...D49
431(chain D and (resid 16 through 47 or resid 49...D51 - 60
441(chain D and (resid 16 through 47 or resid 49...D71 - 74
451(chain D and (resid 16 through 47 or resid 49...D76
461(chain D and (resid 16 through 47 or resid 49...D226 - 283
471(chain D and (resid 16 through 47 or resid 49...D291 - 383

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Components

#1: Protein
SAVED domain-containing protein


Mass: 44606.578 Da / Num. of mol.: 4
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 4.28 Å3/Da / Density % sol: 71.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12-15% PEG6000, 100 mM sodium citrate, pH 5.5, 100 mM NaCl

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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: RAYONIX MX300-HS / Detector: CCD / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 41618 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.2
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 4116 / CC1/2: 0.85

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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: 3.4→45.19 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2955 1993 4.79 %
Rwork0.2488 39625 -
obs0.251 41618 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.87 Å2 / Biso mean: 87.3465 Å2 / Biso min: 41.32 Å2
Refinement stepCycle: final / Resolution: 3.4→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11427 0 4 0 11431
Biso mean--83.43 --
Num. residues----1413
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4084X-RAY DIFFRACTION6.962TORSIONAL
12B4084X-RAY DIFFRACTION6.962TORSIONAL
13C4084X-RAY DIFFRACTION6.962TORSIONAL
14D4084X-RAY DIFFRACTION6.962TORSIONAL
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 (%)
3.4-3.490.37141440.272228132957100
3.49-3.580.35391410.267628292970100
3.58-3.680.3051420.259827892931100
3.68-3.80.30251450.24128022947100
3.8-3.940.31241410.242528472988100
3.94-4.10.27711400.220627952935100
4.1-4.280.24521390.235228422981100
4.28-4.510.30281440.209328532997100
4.51-4.790.24721410.221328052946100
4.79-5.160.25461450.220428402985100
5.16-5.680.28021430.259528603003100
5.68-6.50.32821380.276128452983100
6.5-8.180.31441480.278128733021100
8.18-45.190.30991420.26862832297496
Refinement TLS params.Method: refined / Origin x: 34.6083 Å / Origin y: -55.7309 Å / Origin z: 15.639 Å
111213212223313233
T0.6382 Å20.0698 Å2-0.049 Å2-0.6517 Å20.0084 Å2--0.6058 Å2
L0.2347 °2-0.3253 °2-0.1084 °2-0.3187 °20.0283 °2---0.1504 °2
S0.0861 Å °0.148 Å °-0.0446 Å °-0.1472 Å °-0.1359 Å °0.1258 Å °-0.0011 Å °0.0024 Å °0.0548 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA16 - 383
2X-RAY DIFFRACTION1allB16 - 383
3X-RAY DIFFRACTION1allC16 - 383
4X-RAY DIFFRACTION1allD16 - 383
5X-RAY DIFFRACTION1allM1 - 4

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