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- PDB-6m37: The crystal structure of B. subtilis RsbV/RsbW complex in the hex... -

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Basic information

Entry
Database: PDB / ID: 6m37
TitleThe crystal structure of B. subtilis RsbV/RsbW complex in the hexagonal crystal form
Components
  • Anti-sigma-B factor antagonist
  • Serine-protein kinase RsbW
KeywordsSIGNALING PROTEIN / sigma factor / anti-sigma / anti-anti-sigma / SigB / RsbW / RsbV
Function / homology
Function and homology information


anti-sigma factor antagonist activity / sigma factor antagonist activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity ...anti-sigma factor antagonist activity / sigma factor antagonist activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding
Similarity search - Function
Serine-protein kinase RsbW / : / Histidine kinase-like ATPase domain / Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily ...Serine-protein kinase RsbW / : / Histidine kinase-like ATPase domain / Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Anti-sigma-B factor antagonist / Serine-protein kinase RsbW
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPathak, D. / Kwon, E. / Kim, D.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017R1D1A1B03034088 Korea, Republic Of
National Research Foundation (NRF, Korea)2017R1A6A3A11029218 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Structural insights into the regulation of SigB activity by RsbV and RsbW.
Authors: Pathak, D. / Jin, K.S. / Tandukar, S. / Kim, J.H. / Kwon, E. / Kim, D.Y.
History
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine-protein kinase RsbW
B: Anti-sigma-B factor antagonist
C: Serine-protein kinase RsbW
D: Anti-sigma-B factor antagonist


Theoretical massNumber of molelcules
Total (without water)54,1054
Polymers54,1054
Non-polymers00
Water00
1
A: Serine-protein kinase RsbW
B: Anti-sigma-B factor antagonist
C: Serine-protein kinase RsbW
D: Anti-sigma-B factor antagonist

A: Serine-protein kinase RsbW
B: Anti-sigma-B factor antagonist
C: Serine-protein kinase RsbW
D: Anti-sigma-B factor antagonist


Theoretical massNumber of molelcules
Total (without water)108,2108
Polymers108,2108
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z1
Unit cell
Length a, b, c (Å)158.200, 158.200, 96.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 6 through 144)
21(chain C and (resid 6 through 85 or resid 113 through 144))
12(chain B and resid 2 through 101)
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPASNASN(chain A and resid 6 through 144)AA6 - 1442 - 140
211ASPASPGLUGLU(chain C and (resid 6 through 85 or resid 113 through 144))CC6 - 852 - 81
221GLYGLYASNASN(chain C and (resid 6 through 85 or resid 113 through 144))CC113 - 144109 - 140
112ASNASNSERSER(chain B and resid 2 through 101)BB2 - 1011 - 100
212ASNASNSERSERchain DDD2 - 1011 - 100

NCS ensembles :
ID
1
2

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Components

#1: Protein Serine-protein kinase RsbW / Anti-sigma-B factor / Sigma-B negative effector RsbW


Mass: 15702.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rsbW, BSU04720 / Production host: Escherichia coli (E. coli)
References: UniProt: P17904, non-specific serine/threonine protein kinase
#2: Protein Anti-sigma-B factor antagonist / Anti-anti-sigma-B factor


Mass: 11350.083 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rsbV, BSU04710 / Production host: Escherichia coli (E. coli) / References: UniProt: P17903

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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: 3.22 Å3/Da / Density % sol: 61.86 % / Description: Rod-shaped hexagonal crystal
Crystal growTemperature: 293 K / Method: batch mode / Details: 20% w/v PEG3350 and 200 mM Potassium formate, ADP

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 13426 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 87.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.3
Reflection shellResolution: 3.1→3.31 Å / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2377

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Processing

Software
NameVersionClassification
PHENIXdev_3051refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THN, 1TIL

1thn

1til


Resolution: 3.1→45.668 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 653 4.87 %
Rwork0.2216 12750 -
obs0.2232 13403 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.25 Å2 / Biso mean: 80.5029 Å2 / Biso min: 41.93 Å2
Refinement stepCycle: final / Resolution: 3.1→45.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 0 0 3333
Num. residues----429
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A660X-RAY DIFFRACTION8.947TORSIONAL
12C660X-RAY DIFFRACTION8.947TORSIONAL
21B602X-RAY DIFFRACTION8.947TORSIONAL
22D602X-RAY DIFFRACTION8.947TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.1001-3.33940.33251250.28942491
3.3394-3.67530.24881300.22532495
3.6753-4.20680.25851350.21652512
4.2068-5.29890.22851340.19762553
5.2989-45.6680.25071290.22722699

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