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- PDB-8t9n: Bacillus subtilis RsgI GGG mutant -

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Basic information

Entry
Database: PDB / ID: 8t9n
TitleBacillus subtilis RsgI GGG mutant
ComponentsAnti-sigma-I factor RsgI
KeywordsMEMBRANE PROTEIN / Autoproteolysis / SEA domain / mechanotransduction / regulated intramembrane proteolysis (RIP) / adhesion GPCR / cellulosomes / SigI/RsgI
Function / homologyAnti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / plasma membrane / Anti-sigma-I factor RsgI
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrogan, A.P. / Habib, C. / Hobbs, S.J. / Kranzusch, P.J. / Rudner, D.Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Bacterial SEAL domains undergo autoproteolysis and function in regulated intramembrane proteolysis.
Authors: Brogan, A.P. / Habib, C. / Hobbs, S.J. / Kranzusch, P.J. / Rudner, D.Z.
History
DepositionJun 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-sigma-I factor RsgI
B: Anti-sigma-I factor RsgI


Theoretical massNumber of molelcules
Total (without water)30,8362
Polymers30,8362
Non-polymers00
Water1,58588
1
A: Anti-sigma-I factor RsgI


Theoretical massNumber of molelcules
Total (without water)15,4181
Polymers15,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-sigma-I factor RsgI


Theoretical massNumber of molelcules
Total (without water)15,4181
Polymers15,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.175, 63.889, 59.935
Angle α, β, γ (deg.)90.000, 92.660, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Anti-sigma-I factor RsgI / Regulation of sigma I protein


Mass: 15418.164 Da / Num. of mol.: 2 / Mutation: Extra glycine in loop containing residues 11-13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rsgI, ykrI, BSU13460 / Production host: Escherichia coli (E. coli) / References: UniProt: O31655
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES-KOH pH 7.5, 100 mM ammonium acetate, 28.5% PEG-3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→38.13 Å / Num. obs: 22424 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.27 Å2 / Rpim(I) all: 0.028 / Net I/σ(I): 10.1
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1431 / Rpim(I) all: 0.655

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.13 Å / SU ML: 0.2772 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.4228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 1994 8.99 %
Rwork0.2303 20190 -
obs0.2343 22184 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 0 88 2071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422009
X-RAY DIFFRACTIONf_angle_d0.68782709
X-RAY DIFFRACTIONf_chiral_restr0.0455309
X-RAY DIFFRACTIONf_plane_restr0.0045344
X-RAY DIFFRACTIONf_dihedral_angle_d4.8163264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.3881290.37841313X-RAY DIFFRACTION89.45
1.95-20.3771420.32891465X-RAY DIFFRACTION97.1
2-2.060.34381380.29351411X-RAY DIFFRACTION97.67
2.06-2.130.34941520.29341443X-RAY DIFFRACTION97.43
2.13-2.20.33171380.26711421X-RAY DIFFRACTION97.68
2.2-2.290.29861310.27311403X-RAY DIFFRACTION95.46
2.29-2.390.33431530.27111462X-RAY DIFFRACTION98.42
2.39-2.520.31621440.2521438X-RAY DIFFRACTION98.81
2.52-2.680.26981430.2581482X-RAY DIFFRACTION98.48
2.68-2.880.30321510.25081439X-RAY DIFFRACTION98.45
2.88-3.170.30021360.25351480X-RAY DIFFRACTION98.36
3.18-3.630.27671410.22941434X-RAY DIFFRACTION97.64
3.63-4.580.24771430.19911507X-RAY DIFFRACTION99.76
4.58-38.130.23311530.1951492X-RAY DIFFRACTION98.33
Refinement TLS params.Method: refined / Origin x: 12.0052973767 Å / Origin y: 0.7285083783 Å / Origin z: 18.5458867018 Å
111213212223313233
T0.449839801465 Å20.0129601254432 Å2-0.0987079765264 Å2-0.454010055179 Å20.00283180857906 Å2--0.45223084731 Å2
L1.71000081528 °20.496946746373 °23.47900508126 °2-0.107953186773 °20.502716098435 °2--6.07967228409 °2
S-0.07691880795 Å °0.134782347323 Å °-0.0117226117106 Å °0.10675763076 Å °0.0373720547801 Å °-0.0635447162299 Å °-0.141704110716 Å °0.45775786524 Å °-0.0462077733262 Å °
Refinement TLS groupSelection details: all

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