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- PDB-7lq2: Apo Rr RsiG- crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 7lq2
TitleApo Rr RsiG- crystal form 1
ComponentsRR RsiG
KeywordsTRANSCRIPTION / RsiG / single-motif / WhiG / evolution / homodimer / Rubrobacter radiotolerans
Function / homology: / RsiG-like / nucleotide binding / metal ion binding / ISOPROPYL ALCOHOL / RsiG-like domain-containing protein
Function and homology information
Biological speciesRubrobacter radiotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RR RsiG
C: RR RsiG
F: RR RsiG
E: RR RsiG
D: RR RsiG
A: RR RsiG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24410
Polymers58,0756
Non-polymers1694
Water7,981443
1
B: RR RsiG
C: RR RsiG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5035
Polymers19,3582
Non-polymers1443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-35 kcal/mol
Surface area10280 Å2
MethodPISA
2
F: RR RsiG
E: RR RsiG


Theoretical massNumber of molelcules
Total (without water)19,3582
Polymers19,3582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-31 kcal/mol
Surface area9370 Å2
MethodPISA
3
D: RR RsiG
A: RR RsiG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3833
Polymers19,3582
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-32 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.479, 95.293, 117.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
RR RsiG


Mass: 9679.238 Da / Num. of mol.: 6
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 12% isopropanol, 0.1 M HEPES pH 7.5, 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 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→50.46 Å / Num. obs: 57371 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rpim(I) all: 0.032 / Rsym value: 0.053 / Net I/σ(I): 17.8
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5313 / CC1/2: 0.898 / Rpim(I) all: 0.374 / Rsym value: 0.464

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACT3.27data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→50.457 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1672 2.92 %
Rwork0.1736 55625 -
obs0.1745 57297 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.01 Å2 / Biso mean: 28.1805 Å2 / Biso min: 10.33 Å2
Refinement stepCycle: final / Resolution: 1.85→50.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 10 444 3928
Biso mean--15.59 40.58 -
Num. residues----436
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.90440.27361270.2275424892
1.9044-1.96590.23721370.2017455599
1.9659-2.03620.24661390.18864613100
2.0362-2.11770.20861390.16984612100
2.1177-2.21410.19661390.16254607100
2.2141-2.33080.20381390.16214628100
2.3308-2.47680.1961390.17114646100
2.4768-2.66810.18381410.16824672100
2.6681-2.93650.2181400.17554667100
2.9365-3.36140.20631420.17364696100
3.3614-4.23470.1791420.1614757100
4.2347-50.4570.19831480.1797492499
Refinement TLS params.Method: refined / Origin x: 44.5479 Å / Origin y: 22.0469 Å / Origin z: 66.4727 Å
111213212223313233
T0.0757 Å20.0006 Å2-0.0024 Å2-0.0541 Å20.0017 Å2--0.089 Å2
L0.2052 °20.0264 °20.1531 °2--0.0394 °20.0795 °2--1.0327 °2
S0.0017 Å °-0.0046 Å °-0.0047 Å °0.0068 Å °-0.0022 Å °-0.0002 Å °0.0034 Å °-0.0064 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB23 - 98
2X-RAY DIFFRACTION1allC23 - 98
3X-RAY DIFFRACTION1allF28 - 98
4X-RAY DIFFRACTION1allE28 - 98
5X-RAY DIFFRACTION1allD28 - 98
6X-RAY DIFFRACTION1allA28 - 98
7X-RAY DIFFRACTION1allS1 - 457
8X-RAY DIFFRACTION1allT2002 - 2003

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