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- PDB-5wuq: Crystal structure of SigW in complex with its anti-sigma RsiW, a ... -

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Basic information

Entry
Database: PDB / ID: 5wuq
TitleCrystal structure of SigW in complex with its anti-sigma RsiW, a zinc binding form
Components
  • Anti-sigma-W factor RsiW
  • ECF RNA polymerase sigma factor SigW
KeywordsMETAL BINDING PROTEIN / sigma-anti-sigma complex / zinc binding motif
Function / homology
Function and homology information


response to stress / sigma factor activity / DNA-templated transcription initiation / regulation of DNA-templated transcription / DNA binding / metal ion binding / plasma membrane
Similarity search - Function
RNA polymerase sigma-W, bacillaceae / Anti-sigma factor, zinc-finger domain superfamily / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 2 ...RNA polymerase sigma-W, bacillaceae / Anti-sigma factor, zinc-finger domain superfamily / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ECF RNA polymerase sigma factor SigW / Anti-sigma-W factor RsiW
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDevkota, S.R. / Kwon, E. / Ha, S.C. / Kim, D.Y.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural insights into the regulation of Bacillus subtilis SigW activity by anti-sigma RsiW
Authors: Devkota, S.R. / Kwon, E. / Ha, S.C. / Chang, H.W. / Kim, D.Y.
History
DepositionDec 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ECF RNA polymerase sigma factor SigW
B: ECF RNA polymerase sigma factor SigW
C: Anti-sigma-W factor RsiW
D: Anti-sigma-W factor RsiW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0596
Polymers61,9284
Non-polymers1312
Water00
1
A: ECF RNA polymerase sigma factor SigW
C: Anti-sigma-W factor RsiW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0293
Polymers30,9642
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-17 kcal/mol
Surface area12690 Å2
MethodPISA
2
B: ECF RNA polymerase sigma factor SigW
D: Anti-sigma-W factor RsiW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0293
Polymers30,9642
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-19 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.462, 64.206, 138.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ECF RNA polymerase sigma factor SigW / ECF sigma factor SigW / Alternative RNA polymerase sigma factor SigW / RNA polymerase sigma-W ...ECF sigma factor SigW / Alternative RNA polymerase sigma factor SigW / RNA polymerase sigma-W factor / Sigma-W factor


Mass: 21745.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: sigW / Plasmid: pET-DUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q45585
#2: Protein Anti-sigma-W factor RsiW / Regulator of SigW / Sigma-W anti-sigma factor RsiW


Mass: 9218.724 Da / Num. of mol.: 2 / Fragment: UNP residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: rsiW / Plasmid: pET-DUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q45588
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5 / Details: PEG3350, isopropanol, calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 14411 / % possible obs: 98.9 % / Redundancy: 5.6 % / Net I/σ(I): 41.5
Reflection shellResolution: 2.8→2.85 Å / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.861 / SU B: 33.568 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28667 662 4.6 %RANDOM
Rwork0.21011 ---
obs0.21359 13669 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 84.855 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å20 Å2
2--0.94 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: 1 / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 2 0 3736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193793
X-RAY DIFFRACTIONr_bond_other_d0.0020.023812
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9745098
X-RAY DIFFRACTIONr_angle_other_deg0.95438770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2645446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.06623.956182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75715765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7931530
X-RAY DIFFRACTIONr_chiral_restr0.070.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02837
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7415.6761802
X-RAY DIFFRACTIONr_mcbond_other1.7425.6751801
X-RAY DIFFRACTIONr_mcangle_it2.9088.5082242
X-RAY DIFFRACTIONr_mcangle_other2.9078.5092243
X-RAY DIFFRACTIONr_scbond_it1.7745.8781991
X-RAY DIFFRACTIONr_scbond_other1.7745.8791992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0348.7342857
X-RAY DIFFRACTIONr_long_range_B_refined4.62343.4394207
X-RAY DIFFRACTIONr_long_range_B_other4.62243.4474208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 41 -
Rwork0.253 994 -
obs--99.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.73151.5052-1.77583.05950.07624.1509-0.0922-0.3062-0.2905-0.0070.05120.1437-0.11920.40320.0410.0313-0.0024-0.00430.10420.00210.0653-20.16980.824618.2849
23.36720.06380.6711.55620.0195.57510.34070.1971-0.0192-0.0709-0.15890.1847-0.68580.0081-0.18180.23140.09350.06320.07880.0110.057-19.9036-0.0992-19.0043
34.52321.9433-2.83135.217-2.03193.87790.33440.15320.1397-0.0925-0.0401-0.1255-0.54280.5488-0.29420.2704-0.17610.02150.2403-0.04750.055-11.661911.23814.989
45.9354-3.41113.11854.1536-1.66326.15660.1681-0.44230.09350.1490.134-0.3070.26350.5339-0.30210.13260.08120.03930.23920.01410.1185-8.5443-7.8536-5.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 187
2X-RAY DIFFRACTION2B3 - 187
3X-RAY DIFFRACTION3C3 - 72
4X-RAY DIFFRACTION4D3 - 71

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