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- PDB-6m36: The crystal structure of B. subtilis RsbV/RsbW complex in the mon... -

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Basic information

Entry
Database: PDB / ID: 6m36
TitleThe crystal structure of B. subtilis RsbV/RsbW complex in the monoclinic 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 / negative regulation of DNA-templated transcription / 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: 3.4 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

Downloads & links

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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
E: Serine-protein kinase RsbW
F: Anti-sigma-B factor antagonist
G: Serine-protein kinase RsbW
H: Anti-sigma-B factor antagonist
I: Serine-protein kinase RsbW
J: Anti-sigma-B factor antagonist
K: Serine-protein kinase RsbW
L: Anti-sigma-B factor antagonist
M: Serine-protein kinase RsbW
N: Anti-sigma-B factor antagonist
O: Serine-protein kinase RsbW
P: Anti-sigma-B factor antagonist


Theoretical massNumber of molelcules
Total (without water)216,42016
Polymers216,42016
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
E: Serine-protein kinase RsbW
F: Anti-sigma-B factor antagonist
G: Serine-protein kinase RsbW
H: 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
2
I: Serine-protein kinase RsbW
J: Anti-sigma-B factor antagonist
K: Serine-protein kinase RsbW
L: Anti-sigma-B factor antagonist
M: Serine-protein kinase RsbW
N: Anti-sigma-B factor antagonist
O: Serine-protein kinase RsbW
P: 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
Unit cell
Length a, b, c (Å)117.230, 70.940, 137.680
Angle α, β, γ (deg.)90.000, 105.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))
21(chain C and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))
31(chain E and (resid 8 through 56 or resid 66 through 143))
41(chain G and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))
51(chain I and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))
61(chain K and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))
71(chain M and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))
81(chain O and (resid 8 through 56 or resid 66 through 143))
12(chain B and (resid 2 through 39 or resid 43 through 99))
22(chain D and (resid 2 through 39 or resid 43 through 99))
32chain F
42(chain H and (resid 2 through 39 or resid 43 through 99))
52(chain J and (resid 2 through 39 or resid 43 through 99))
62(chain L and (resid 2 through 39 or resid 43 through 99))
72(chain N and (resid 2 through 39 or resid 43 through 99))
82(chain P and (resid 2 through 39 or resid 43 through 99))

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
111ILEILEGLNGLN(chain A and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))AA8 - 564 - 52
121GLUGLUASNASN(chain A and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))AA66 - 13162 - 127
131GLYGLYLEULEU(chain A and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))AA134 - 143130 - 139
211ILEILEGLNGLN(chain C and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))CC8 - 564 - 52
221GLUGLUASNASN(chain C and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))CC66 - 13162 - 127
231GLYGLYLEULEU(chain C and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))CC134 - 143130 - 139
311ILEILEGLNGLN(chain E and (resid 8 through 56 or resid 66 through 143))EE8 - 564 - 52
321GLUGLULEULEU(chain E and (resid 8 through 56 or resid 66 through 143))EE66 - 14362 - 139
411ILEILEGLNGLN(chain G and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))GG8 - 564 - 52
421GLUGLUASNASN(chain G and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))GG66 - 13162 - 127
431GLYGLYLEULEU(chain G and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))GG134 - 143130 - 139
511ILEILEGLNGLN(chain I and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))II8 - 564 - 52
521GLUGLUASNASN(chain I and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))II66 - 13162 - 127
531GLYGLYLEULEU(chain I and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))II134 - 143130 - 139
611ILEILEGLNGLN(chain K and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))KK8 - 564 - 52
621GLUGLUASNASN(chain K and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))KK66 - 13162 - 127
631GLYGLYLEULEU(chain K and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))KK134 - 143130 - 139
711ILEILEGLNGLN(chain M and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))MM8 - 564 - 52
721GLUGLUASNASN(chain M and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))MM66 - 13162 - 127
731GLYGLYLEULEU(chain M and (resid 8 through 56 or resid 66 through 131 or resid 134 through 143))MM134 - 143130 - 139
811ILEILEGLNGLN(chain O and (resid 8 through 56 or resid 66 through 143))OO8 - 564 - 52
821GLUGLULEULEU(chain O and (resid 8 through 56 or resid 66 through 143))OO66 - 14362 - 139
112ASNASNGLUGLU(chain B and (resid 2 through 39 or resid 43 through 99))BB2 - 391 - 38
122ASPASPASPASP(chain B and (resid 2 through 39 or resid 43 through 99))BB43 - 9942 - 98
212ASNASNGLUGLU(chain D and (resid 2 through 39 or resid 43 through 99))DD2 - 391 - 38
222ASPASPASPASP(chain D and (resid 2 through 39 or resid 43 through 99))DD43 - 9942 - 98
312ASNASNASPASPchain FFF2 - 991 - 98
412ASNASNGLUGLU(chain H and (resid 2 through 39 or resid 43 through 99))HH2 - 391 - 38
422ASPASPASPASP(chain H and (resid 2 through 39 or resid 43 through 99))HH43 - 9942 - 98
512ASNASNGLUGLU(chain J and (resid 2 through 39 or resid 43 through 99))JJ2 - 391 - 38
522ASPASPASPASP(chain J and (resid 2 through 39 or resid 43 through 99))JJ43 - 9942 - 98
612ASNASNGLUGLU(chain L and (resid 2 through 39 or resid 43 through 99))LL2 - 391 - 38
622ASPASPASPASP(chain L and (resid 2 through 39 or resid 43 through 99))LL43 - 9942 - 98
712ASNASNGLUGLU(chain N and (resid 2 through 39 or resid 43 through 99))NN2 - 391 - 38
722ASPASPASPASP(chain N and (resid 2 through 39 or resid 43 through 99))NN43 - 9942 - 98
812ASNASNGLUGLU(chain P and (resid 2 through 39 or resid 43 through 99))PP2 - 391 - 38
822ASPASPASPASP(chain P and (resid 2 through 39 or resid 43 through 99))PP43 - 9942 - 98

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.: 8
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.: 8
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: 2.55 Å3/Da / Density % sol: 51.78 % / Description: plate-shaped monoclinic crystal
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.5 / Details: 25% w/v PEG 1500 and 100 mM SPG buffer

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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: 3.4→48.47 Å / Num. obs: 29346 / % possible obs: 96.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 71.21 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 6.8
Reflection shellResolution: 3.4→3.61 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.4 / 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: 3.4→29.788 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2903 1465 5.01 %
Rwork0.2074 27753 -
obs0.2115 29218 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.75 Å2 / Biso mean: 68.0497 Å2 / Biso min: 25.12 Å2
Refinement stepCycle: final / Resolution: 3.4→29.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12580 0 0 0 12580
Num. residues----1619
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2248X-RAY DIFFRACTION11.442TORSIONAL
12C2248X-RAY DIFFRACTION11.442TORSIONAL
13E2248X-RAY DIFFRACTION11.442TORSIONAL
14G2248X-RAY DIFFRACTION11.442TORSIONAL
15I2248X-RAY DIFFRACTION11.442TORSIONAL
16K2248X-RAY DIFFRACTION11.442TORSIONAL
17M2248X-RAY DIFFRACTION11.442TORSIONAL
18O2248X-RAY DIFFRACTION11.442TORSIONAL
21B2264X-RAY DIFFRACTION11.442TORSIONAL
22D2264X-RAY DIFFRACTION11.442TORSIONAL
23F2264X-RAY DIFFRACTION11.442TORSIONAL
24H2264X-RAY DIFFRACTION11.442TORSIONAL
25J2264X-RAY DIFFRACTION11.442TORSIONAL
26L2264X-RAY DIFFRACTION11.442TORSIONAL
27N2264X-RAY DIFFRACTION11.442TORSIONAL
28P2264X-RAY DIFFRACTION11.442TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.52140.34981410.2852264692
3.5214-3.66210.36681480.2541273597
3.6621-3.82850.31111440.2477278197
3.8285-4.02990.3341590.2285278197
4.0299-4.28170.27361520.1997280197
4.2817-4.61110.26971370.1791267593
4.6111-5.07310.28981560.1823286998
5.0731-5.80250.27041460.2013283398
5.8025-7.29280.29921480.2321273994
7.2928-29.7880.23821340.1727289396

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