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- PDB-7lq3: Evolution of a sigma-(c-di-GMP)-antisigma switch -

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Basic information

Entry
Database: PDB / ID: 7lq3
TitleEvolution of a sigma-(c-di-GMP)-antisigma switch
ComponentsRsiG
KeywordsTRANSCRIPTION / RsiG / WhiG / Rubrobacter radiotolerans / c-di-GMP / evolution / homonymer
Function / homologyRsiG-like / nucleotide binding / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesRubrobacter radiotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsSchumacher, M.A. / Brennan, R.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Evolution of a sigma-(c-di-GMP)-anti-sigma switch.
Authors: Schumacher, M.A. / Gallagher, K.A. / Holmes, N.A. / Chandra, G. / Henderson, M. / Kysela, D.T. / Brennan, R.G. / Buttner, M.J.
History
DepositionFeb 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RsiG
A: RsiG
D: RsiG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4927
Polymers29,2513
Non-polymers2414
Water18010
1
B: RsiG
A: RsiG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6455
Polymers19,5012
Non-polymers1453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-38 kcal/mol
Surface area9300 Å2
MethodPISA
2
D: RsiG
hetero molecules

D: RsiG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6934
Polymers19,5012
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4010 Å2
ΔGint-66 kcal/mol
Surface area9080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.545, 78.545, 81.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

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Components

#1: Protein RsiG


Mass: 9750.317 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubrobacter radiotolerans (bacteria) / Gene: RradSPS_1442 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023X3Z4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.5, 2.5 M NaCl, 0.2 M lithium sulfate, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→39.273 Å / Num. obs: 8738 / % possible obs: 99.6 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rpim(I) all: 0.028 / Rsym value: 0.087 / Net I/σ(I): 20.2
Reflection shellResolution: 2.55→2.59 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 847 / CC1/2: 0.804 / Rpim(I) all: 0.453 / Rsym value: 1.056

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LQ2

7lq2


Resolution: 2.55→39.273 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 879 10.06 %
Rwork0.1985 7859 -
obs0.2057 8738 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.41 Å2 / Biso mean: 68.5614 Å2 / Biso min: 33.31 Å2
Refinement stepCycle: final / Resolution: 2.55→39.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 12 10 1723
Biso mean--92.96 55.52 -
Num. residues----213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5502-2.70990.31681450.23391272
2.7099-2.91910.28011450.24041279
2.9191-3.21270.2871420.2281279
3.2127-3.67730.28511410.20511305
3.6773-4.63190.25361520.17131319
4.6319-39.2730.25671540.19471405
Refinement TLS params.Method: refined / Origin x: 25.4006 Å / Origin y: 60.9427 Å / Origin z: 21.7989 Å
111213212223313233
T0.3638 Å2-0.0382 Å2-0.0132 Å2-0.2517 Å20.0077 Å2--0.4327 Å2
L1.8732 °20.6859 °20.1617 °2-1.5308 °2-0.4835 °2--4.1108 °2
S-0.1266 Å °0.1543 Å °0.226 Å °0.1686 Å °-0.1339 Å °0.0171 Å °-0.4967 Å °0.2567 Å °0.2395 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB28 - 98
2X-RAY DIFFRACTION1allA28 - 98
3X-RAY DIFFRACTION1allD28 - 98
4X-RAY DIFFRACTION1allI32 - 21
5X-RAY DIFFRACTION1allM2 - 1
6X-RAY DIFFRACTION1allS1 - 10

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