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- PDB-7lq4: Rr (RsiG)2-(c-di-GMP)2-WhiG complex -

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Basic information

Entry
Database: PDB / ID: 7lq4
TitleRr (RsiG)2-(c-di-GMP)2-WhiG complex
Components
  • RsiG
  • WhiG
KeywordsTRANSCRIPTION / RsiG / WhiG / Rubrobacter radiotolerans / c-di-GMP / sigma / anti-sigma / evolution / coiled coil
Function / homologynucleotide binding / metal ion binding / Chem-C2E / Uncharacterized protein
Function and homology information
Biological speciesRubrobacter radiotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: RsiG
T: RsiG
A: WhiG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4745
Polymers48,0943
Non-polymers1,3812
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-51 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.466, 81.621, 114.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RsiG


Mass: 12955.107 Da / Num. of mol.: 2
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: Protein WhiG


Mass: 22183.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubrobacter radiotolerans (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThe complete sequence of WhiG is VRVSIERLWSQYFEARAKLGSLEPDEREAAETLEKRVRGLKDRLVVNYSPLVKYAAGRVT ...The complete sequence of WhiG is VRVSIERLWSQYFEARAKLGSLEPDEREAAETLEKRVRGLKDRLVVNYSPLVKYAAGRVT ARSTGAVDQEEILSWGILGLLDAVETFDAGKGAKFETYAISKIKWAILDELRRLDPLPRR ERQRARESQRARDQLEQRLRRAPTEGEVAREMGVDERDHRSFLNRYRQAQTLSLESGAES ESENGFELHQVIADHLYQTPHEAAEIEELRRNLVEAIKNLAERERLVTTFYFYEGLTLRE IGKALGLTEGRISQILRQSLGKLRDSLSEPRTS

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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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 8.0, 0.2 M MgCl2, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.01 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.9→66.48 Å / Num. obs: 9237 / % possible obs: 91.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 81.78 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Rsym value: 0.043 / Net I/σ(I): 17.1
Reflection shellResolution: 2.93→3.04 Å / Num. unique obs: 601 / CC1/2: 0.804 / Rpim(I) all: 0.23 / Rsym value: 0.24

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PFJ

6pfj


Resolution: 2.9→66.48 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 545 5.9 %
Rwork0.2672 8692 -
obs0.2673 9237 90.88 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.018 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 223.53 Å2 / Biso mean: 106.07 Å2 / Biso min: 38.43 Å2
Baniso -1Baniso -2Baniso -3
1-14.688 Å20 Å2-0 Å2
2--26.5939 Å20 Å2
3----41.2819 Å2
Refinement stepCycle: final / Resolution: 2.9→66.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 92 12 2768
Biso mean--83.2 67.87 -
Num. residues----343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022795
X-RAY DIFFRACTIONf_angle_d0.4773782
X-RAY DIFFRACTIONf_chiral_restr0.04432
X-RAY DIFFRACTIONf_plane_restr0.001473
X-RAY DIFFRACTIONf_dihedral_angle_d15.3261030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9002-3.19210.41521070.3553161770
3.1921-3.65390.30571630.3105227698
3.6539-4.60340.25361270.2574234898
4.6034-66.480.2451480.245245198
Refinement TLS params.Method: refined / Origin x: -17.0899 Å / Origin y: -4.8801 Å / Origin z: -24.5724 Å
111213212223313233
T0.2884 Å20.0252 Å20.0296 Å2-0.3108 Å20.0435 Å2--0.3251 Å2
L0.3787 °20.225 °2-0.3295 °2-1.1572 °2-0.8487 °2--1.9023 °2
S-0.0523 Å °0.0716 Å °0.0027 Å °0.1205 Å °0.0107 Å °-0.0122 Å °-0.1236 Å °0.0312 Å °0.0389 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allD23 - 99
2X-RAY DIFFRACTION1allT28 - 101
3X-RAY DIFFRACTION1allA2 - 271
4X-RAY DIFFRACTION1allS1 - 12
5X-RAY DIFFRACTION1allR203 - 201

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