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

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Basic information

Entry
Database: PDB / ID: 5wur
TitleCrystal structure of SigW in complex with its anti-sigma RsiW, an oxdized 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


sigma factor activity / response to stress / DNA-templated transcription initiation / regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / metal ion binding / plasma membrane
Similarity search - Function
RNA polymerase sigma-W, bacillaceae / Putative zinc-finger / Putative zinc-finger / Anti-sigma factor, zinc-finger domain superfamily / RNA polymerase sigma factor 70, region 4 type 2 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / Sigma-70, region 4 / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 2 ...RNA polymerase sigma-W, bacillaceae / Putative zinc-finger / Putative zinc-finger / Anti-sigma factor, zinc-finger domain superfamily / RNA polymerase sigma factor 70, region 4 type 2 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / Sigma-70, region 4 / 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: 2.6 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 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)61,9284
Polymers61,9284
Non-polymers00
Water00
1
A: ECF RNA polymerase sigma factor SigW
C: Anti-sigma-W factor RsiW


Theoretical massNumber of molelcules
Total (without water)30,9642
Polymers30,9642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-20 kcal/mol
Surface area12520 Å2
MethodPISA
2
B: ECF RNA polymerase sigma factor SigW
D: Anti-sigma-W factor RsiW


Theoretical massNumber of molelcules
Total (without water)30,9642
Polymers30,9642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-15 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.075, 63.520, 138.547
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 / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q45588
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: 2.28 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: 0.97926 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 17578 / % possible obs: 99.1 % / Redundancy: 7 % / Net I/σ(I): 46.3
Reflection shellResolution: 2.6→2.64 Å / Mean I/σ(I) obs: 6.4 / % 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: 2.6→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 30.303 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.926 / ESU R Free: 0.337 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26753 896 5.1 %RANDOM
Rwork0.23654 ---
obs0.23824 16625 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.316 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å20 Å20 Å2
2--1.26 Å2-0 Å2
3----5.53 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 0 0 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193787
X-RAY DIFFRACTIONr_bond_other_d0.0020.023801
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9735091
X-RAY DIFFRACTIONr_angle_other_deg0.96638745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.2423.956182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06815763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9961530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02836
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_it1.5444.9131798
X-RAY DIFFRACTIONr_mcbond_other1.5424.9121797
X-RAY DIFFRACTIONr_mcangle_it2.6797.3572237
X-RAY DIFFRACTIONr_mcangle_other2.6797.3582238
X-RAY DIFFRACTIONr_scbond_it1.4135.0841989
X-RAY DIFFRACTIONr_scbond_other1.4135.0851990
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5077.5482855
X-RAY DIFFRACTIONr_long_range_B_refined4.51637.1414276
X-RAY DIFFRACTIONr_long_range_B_other4.51637.1484277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 70 -
Rwork0.31 1193 -
obs--97.45 %
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)
12.5107-0.854-1.78190.9055-0.21392.807-0.00770.1838-0.10870.1418-0.0192-0.175-0.2292-0.1710.02690.22360.0607-0.05150.19420.0210.3602-11.24821.4676-18.5095
20.6681-0.11110.52210.0827-0.53274.58570.2185-0.3182-0.239-0.0027-0.0129-0.016-0.63930.0009-0.20570.421-0.16460.1090.24490.0590.3736-11.7882-0.579718.9617
32.2248-1.5492-1.2933.18380.98462.23660.0038-0.2797-0.02780.5170.2425-0.1519-0.4546-0.16-0.24630.42280.16020.04910.12920.02610.199-19.523111.2043-4.9089
42.90981.40361.22590.70190.5393.77670.30370.2882-0.16640.1080.1608-0.1523-0.0949-0.6255-0.46450.2398-0.00520.07650.24110.060.3748-22.7565-7.82724.8836
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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