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- PDB-1sc5: Sigma-28(FliA)/FlgM complex -

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Basic information

Entry
Database: PDB / ID: 1sc5
TitleSigma-28(FliA)/FlgM complex
Components
  • RNA polymerase sigma factor FliA
  • anti-sigma factor FlgM
KeywordsTRANSCRIPTION / RNA POLYMERASE SIGMA FACTOR / ANTI-SIGMA FACTOR / FLAGELLAR GENE REGULATION
Function / homology
Function and homology information


antisigma factor binding / sigma factor antagonist activity / sigma factor antagonist complex / molecular function inhibitor activity / sigma factor activity / DNA-templated transcription initiation / transcription coregulator binding / DNA-directed 5'-3' RNA polymerase activity / disordered domain specific binding / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Helix Hairpins - #150 / Anti-sigma-28 factor FlgM / Anti-sigma-28 factor FlgM, C-terminal / Anti-sigma-28 factor FlgM superfamily / Anti-sigma-28 factor, FlgM / RNA polymerase sigma factor, FliA/WhiG / PhyR, sigma-like (SL) domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / Butyryl-CoA Dehydrogenase, subunit A; domain 3 ...Helix Hairpins - #150 / Anti-sigma-28 factor FlgM / Anti-sigma-28 factor FlgM, C-terminal / Anti-sigma-28 factor FlgM superfamily / Anti-sigma-28 factor, FlgM / RNA polymerase sigma factor, FliA/WhiG / PhyR, sigma-like (SL) domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Sigma-70 factors family signature 1. / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / 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 / Helix Hairpins / Helix non-globular / Special / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Anti sigma factor FlgM / RNA polymerase sigma factor FliA
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.26 Å
AuthorsSorenson, M.K. / Ray, S.S. / Darst, S.A.
CitationJournal: Mol.Cell / Year: 2004
Title: Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation.
Authors: Sorenson, M.K. / Ray, S.S. / Darst, S.A.
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase sigma factor FliA
B: anti-sigma factor FlgM


Theoretical massNumber of molelcules
Total (without water)37,9932
Polymers37,9932
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-28 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.117, 118.117, 87.401
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RNA polymerase sigma factor FliA


Mass: 27735.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: FLIA / Plasmid: pKMS5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL-codon(+) / References: UniProt: O67268
#2: Protein anti-sigma factor FlgM


Mass: 10257.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: FLGM / Plasmid: pKMS5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL-codon(+) / References: UniProt: O66683

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.44 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 800, sodium cacodylate, calcium acetate, sodium chloride, tris, isopropanol, 6-amino-caproic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96486,0.97969,0.97989,0.96486
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.964861
20.979691
30.979891
ReflectionResolution: 3.25→30 Å / Num. all: 11003 / Num. obs: 11003 / % possible obs: 96.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.25→3.37 Å / % possible all: 92

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.26→19.92 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 440999.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 555 5.2 %RANDOM
Rwork0.241 ---
all0.243 11003 --
obs0.241 10616 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.7763 Å2 / ksol: 0.227207 e/Å3
Displacement parametersBiso mean: 74.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å27.56 Å20 Å2
2--0.14 Å20 Å2
3----0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.26→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 0 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it13.591.5
X-RAY DIFFRACTIONc_mcangle_it21.182
X-RAY DIFFRACTIONc_scbond_it29.882
X-RAY DIFFRACTIONc_scangle_it36.262.5
LS refinement shellResolution: 3.25→3.45 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 75 5.1 %
Rwork0.34 1389 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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