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- PDB-1rp3: Cocrystal structure of the flagellar sigma/anti-sigma complex, Si... -

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Basic information

Entry
Database: PDB / ID: 1rp3
TitleCocrystal structure of the flagellar sigma/anti-sigma complex, Sigma-28/FlgM
Components
  • RNA polymerase sigma factor SIGMA-28 (FliA)
  • anti sigma factor FlgM
KeywordsTRANSCRIPTION / SIGMA FACTOR
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 / MAD / Resolution: 2.3 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
DepositionDec 2, 2003Deposition 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 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: RNA polymerase sigma factor SIGMA-28 (FliA)
B: anti sigma factor FlgM
C: RNA polymerase sigma factor SIGMA-28 (FliA)
D: anti sigma factor FlgM
E: RNA polymerase sigma factor SIGMA-28 (FliA)
F: anti sigma factor FlgM
G: RNA polymerase sigma factor SIGMA-28 (FliA)
H: anti sigma factor FlgM


Theoretical massNumber of molelcules
Total (without water)151,9718
Polymers151,9718
Non-polymers00
Water1,31573
1
A: RNA polymerase sigma factor SIGMA-28 (FliA)
B: anti sigma factor FlgM


Theoretical massNumber of molelcules
Total (without water)37,9932
Polymers37,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-36 kcal/mol
Surface area15930 Å2
MethodPISA
2
C: RNA polymerase sigma factor SIGMA-28 (FliA)
D: anti sigma factor FlgM


Theoretical massNumber of molelcules
Total (without water)37,9932
Polymers37,9932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-34 kcal/mol
Surface area15590 Å2
MethodPISA
3
E: RNA polymerase sigma factor SIGMA-28 (FliA)
F: anti sigma factor FlgM


Theoretical massNumber of molelcules
Total (without water)37,9932
Polymers37,9932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-32 kcal/mol
Surface area15300 Å2
MethodPISA
4
G: RNA polymerase sigma factor SIGMA-28 (FliA)
H: anti sigma factor FlgM


Theoretical massNumber of molelcules
Total (without water)37,9932
Polymers37,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-31 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.388, 119.666, 100.056
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RNA polymerase sigma factor SIGMA-28 (FliA)


Mass: 27735.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67268
#2: Protein
anti sigma factor FlgM


Mass: 10257.778 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67268, UniProt: O66683*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16.2% PEG 8000, 0.09M SODIUM CACODYLATE, 0.18M CALCIUM ACETATE, 3% ISOPROPANOL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.50

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Data collection

RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 76085 / % possible obs: 99.9 % / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 26.1 Å2 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.92 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / Rfactor Rfree error: 0.005 / SU B: 7.523 / SU ML: 0.178 / Data cutoff high absF: 329601.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3388 4.8 %RANDOM
Rwork0.242 ---
obs0.242 70618 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.6271 Å2 / ksol: 0.31168 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.84 Å20 Å211.35 Å2
2---19.55 Å20 Å2
3---13.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9037 0 0 73 9110
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 437 4.2 %
Rwork0.343 9944 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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