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- PDB-6in7: Crystal structure of AlgU in complex with MucA(cyto) -

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Basic information

Entry
Database: PDB / ID: 6in7
TitleCrystal structure of AlgU in complex with MucA(cyto)
Components
  • RNA polymerase sigma-H factor
  • Sigma factor AlgU negative regulatory protein
KeywordsTRANSCRIPTION / Sigma factor
Function / homology
Function and homology information


positive regulation of cellular response to heat / regulation of polysaccharide biosynthetic process / positive regulation of response to oxidative stress / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of single-species biofilm formation on inanimate substrate / alginic acid biosynthetic process / sigma factor antagonist activity / cellular response to antibiotic / DNA-binding transcription activator activity ...positive regulation of cellular response to heat / regulation of polysaccharide biosynthetic process / positive regulation of response to oxidative stress / negative regulation of bacterial-type flagellum-dependent cell motility / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of single-species biofilm formation on inanimate substrate / alginic acid biosynthetic process / sigma factor antagonist activity / cellular response to antibiotic / DNA-binding transcription activator activity / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / sigma factor activity / protein-DNA complex / DNA-templated transcription initiation / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / Anti sigma-E protein RseA, N-terminal domain / Anti sigma-E protein RseA, C-terminal domain / RNA polymerase sigma-70 RpoE type / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. ...Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / Anti sigma-E protein RseA, N-terminal domain / Anti sigma-E protein RseA, C-terminal domain / RNA polymerase sigma-70 RpoE type / RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / 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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICOTINAMIDE / Sigma factor AlgU negative regulatory protein / RNA polymerase sigma-H factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsLi, S. / Zhang, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570128 China
CitationJournal: Febs J. / Year: 2019
Title: Structural basis for the recognition of MucA by MucB and AlgU in Pseudomonas aeruginosa.
Authors: Li, S. / Lou, X. / Xu, Y. / Teng, X. / Liu, R. / Zhang, Q. / Wu, W. / Wang, Y. / Bartlam, M.
History
DepositionOct 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
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: Sigma factor AlgU negative regulatory protein
B: RNA polymerase sigma-H factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2573
Polymers31,1352
Non-polymers1221
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-28 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.784, 72.256, 81.721
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 Sigma factor AlgU negative regulatory protein


Mass: 8908.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: mucA, PA0763 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38107
#2: Protein RNA polymerase sigma-H factor / Sigma-30


Mass: 22227.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: algU, algT, PA0762 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06198
#3: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0 M ammonium sulfate,0.1 M cacodylate pH 6.5, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977853 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 23934 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rpim(I) all: 0.09 / Net I/σ(I): 27.9
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 9.2 / Num. unique obs: 1053 / Rpim(I) all: 0.276 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OR7

1or7


Resolution: 1.96→45.505 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.04
RfactorNum. reflection% reflection
Rfree0.2011 1153 4.83 %
Rwork0.1777 --
obs0.1789 23861 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→45.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 9 327 2354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062057
X-RAY DIFFRACTIONf_angle_d0.7792775
X-RAY DIFFRACTIONf_dihedral_angle_d11.7511271
X-RAY DIFFRACTIONf_chiral_restr0.041311
X-RAY DIFFRACTIONf_plane_restr0.005367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9595-2.04870.22261590.17262717X-RAY DIFFRACTION98
2.0487-2.15670.2041370.16942796X-RAY DIFFRACTION100
2.1567-2.29180.19541280.16112826X-RAY DIFFRACTION100
2.2918-2.46880.20761600.17022790X-RAY DIFFRACTION100
2.4688-2.71720.20081170.17982871X-RAY DIFFRACTION100
2.7172-3.11030.20961430.1882848X-RAY DIFFRACTION100
3.1103-3.91830.18691640.16672862X-RAY DIFFRACTION100
3.9183-45.51720.20371450.19122998X-RAY DIFFRACTION99

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