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- PDB-7cg8: Structure of the sensor domain (short construct) of the anti-sigm... -

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Basic information

Entry
Database: PDB / ID: 7cg8
TitleStructure of the sensor domain (short construct) of the anti-sigma factor RsgI4 in Pseudobacteroides cellulosolvens
ComponentsAnti-sigma factor RsgI, N-terminal
KeywordsTRANSCRIPTION / Sugar binding protein
Function / homology: / Anti-sigma factor RsgI-like central domain / Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / plasma membrane / ACETATE ION / Anti-sigma factor RsgI, N-terminal
Function and homology information
Biological speciesPseudobacteroides cellulosolvens ATCC 35603 = DSM 2933 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDong, S. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31661143023 China
CitationJournal: To Be Published
Title: Structure of the sensor domain of the anti-sigma factor RsgI4 in Pseudobacteroides cellulosolvens
Authors: Dong, S. / Chen, C. / Feng, Y.
History
DepositionJun 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-sigma factor RsgI, N-terminal
B: Anti-sigma factor RsgI, N-terminal
C: Anti-sigma factor RsgI, N-terminal
D: Anti-sigma factor RsgI, N-terminal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4049
Polymers45,7844
Non-polymers2,6205
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-41 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.590, 71.050, 100.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Anti-sigma factor RsgI, N-terminal


Mass: 11445.965 Da / Num. of mol.: 4 / Fragment: sensor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudobacteroides cellulosolvens ATCC 35603 = DSM 2933 (bacteria)
Gene: Bccel_2225 / Plasmid: pET28a-SMT3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0L6JMH4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H112O28 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 6.5), 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.5→47.96 Å / Num. obs: 120016 / % possible obs: 99.3 % / Redundancy: 3.48 % / Biso Wilson estimate: 15.37 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.074 / Net I/σ(I): 11.44
Reflection shellResolution: 1.5→1.54 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8817 / CC1/2: 0.664 / Rrim(I) all: 0.837 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDS20191211data scaling
PHASER2.8.3phasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CG5

7cg5


Resolution: 1.5→33.49 Å / SU ML: 0.1558 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1879 3801 3.17 %
Rwork0.1599 116198 -
obs0.1608 119999 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 107 580 3876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083387
X-RAY DIFFRACTIONf_angle_d0.89564568
X-RAY DIFFRACTIONf_chiral_restr0.0749528
X-RAY DIFFRACTIONf_plane_restr0.0065554
X-RAY DIFFRACTIONf_dihedral_angle_d13.4859525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.3061350.27584286X-RAY DIFFRACTION98.18
1.52-1.540.28461390.25634247X-RAY DIFFRACTION98.87
1.54-1.560.2191390.24594268X-RAY DIFFRACTION99.01
1.56-1.580.27371430.23254294X-RAY DIFFRACTION98.62
1.58-1.610.28731430.22564333X-RAY DIFFRACTION99.27
1.61-1.630.28841390.21544260X-RAY DIFFRACTION99.1
1.63-1.660.30131410.21414333X-RAY DIFFRACTION98.98
1.66-1.690.23541400.20294246X-RAY DIFFRACTION99.28
1.69-1.720.2161440.20654300X-RAY DIFFRACTION99.06
1.72-1.750.27741370.20174344X-RAY DIFFRACTION99.14
1.75-1.790.20351450.19494284X-RAY DIFFRACTION98.95
1.79-1.820.22381440.18794318X-RAY DIFFRACTION99.44
1.82-1.870.21111420.17974292X-RAY DIFFRACTION99.46
1.87-1.910.22671390.17364296X-RAY DIFFRACTION99.37
1.91-1.970.1661420.164303X-RAY DIFFRACTION99.57
1.97-2.020.20111380.15294316X-RAY DIFFRACTION99.6
2.02-2.090.19111400.15444325X-RAY DIFFRACTION99.51
2.09-2.160.1961400.15154304X-RAY DIFFRACTION99.6
2.16-2.250.17521380.14354314X-RAY DIFFRACTION99.18
2.25-2.350.19121420.14994309X-RAY DIFFRACTION99.42
2.35-2.480.17861350.15254323X-RAY DIFFRACTION99.58
2.48-2.630.19371430.15534342X-RAY DIFFRACTION99.62
2.63-2.830.17621400.14914285X-RAY DIFFRACTION99.39
2.83-3.120.18371460.15734305X-RAY DIFFRACTION99.64
3.12-3.570.15031430.13374341X-RAY DIFFRACTION99.49
3.57-4.50.15431420.13014322X-RAY DIFFRACTION99.75
4.5-33.490.15911420.1494308X-RAY DIFFRACTION99.64

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