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- PDB-8z6g: the AlgU-MucAcyto complex structure in Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 8z6g
Titlethe AlgU-MucAcyto complex structure in Pseudomonas aeruginosa
Components
  • Anti sigma-E RseA, N-terminal domain protein
  • RNA polymerase sigma factor
KeywordsTRANSCRIPTION / Pseudomonas aeruginosa / AlgU / MucA
Function / homology
Function and homology information


sigma factor antagonist activity / sigma factor activity / DNA-templated transcription initiation / DNA binding / 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 ...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-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
Similarity search - Domain/homology
Anti sigma-E RseA, N-terminal domain protein / RNA polymerase sigma factor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.10109691906 Å
AuthorsLi, T. / Wang, Y.Z. / Bao, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32360046 China
CitationJournal: To Be Published
Title: the AlgU-MucAcyto complex structure in Pseudomonas aeruginosa
Authors: Li, T. / Wang, Y.Z. / Bao, R.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti sigma-E RseA, N-terminal domain protein
B: RNA polymerase sigma factor
C: Anti sigma-E RseA, N-terminal domain protein
D: RNA polymerase sigma factor
E: Anti sigma-E RseA, N-terminal domain protein
F: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)99,2716
Polymers99,2716
Non-polymers00
Water3,099172
1
A: Anti sigma-E RseA, N-terminal domain protein
B: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)33,0902
Polymers33,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-27 kcal/mol
Surface area11970 Å2
MethodPISA
2
C: Anti sigma-E RseA, N-terminal domain protein
D: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)33,0902
Polymers33,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-25 kcal/mol
Surface area12160 Å2
MethodPISA
3
E: Anti sigma-E RseA, N-terminal domain protein
F: RNA polymerase sigma factor


Theoretical massNumber of molelcules
Total (without water)33,0902
Polymers33,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-26 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.525, 126.525, 42.841
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein Anti sigma-E RseA, N-terminal domain protein / MucAcyto / Sigma factor AlgU negative regulatory protein


Mass: 9945.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Anti-Sigma Factor MucA / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CSB93_6114, DY940_22820
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2R3IWP1
#2: Protein RNA polymerase sigma factor


Mass: 23145.270 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: extracellular function sigma transcription factor AlgU
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: algU, rpoE, rpoE_2, ALP65_02762, CAZ10_12515, CSB93_6115, DT376_02630, DY940_22815, GNQ48_23050, GUL26_31990, IPC1295_12635, IPC737_23130, PA52Ts2_1752, PAERUG_P19_London_7_VIM_2_05_10_02252
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A5JL21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 10% 2-Propanol,0.1M BICINE, ph8.5 NaOH,30% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 86935 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 31.88 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.051 / Rrim(I) all: 0.146 / Χ2: 1.055 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.184.40.60443300.3180.6950.3070.6820.99997.1
2.18-2.265.50.57244980.6040.8680.2580.630.94899.4
2.26-2.376.30.51344220.7720.9330.2140.5581.00599.9
2.37-2.496.30.43144510.8720.9650.1790.4681.04299.6
2.49-2.657.20.37744680.9310.9820.1440.4041.04699.7
2.65-2.857.60.28744570.9740.9930.1060.3071.10999.6
2.85-3.147.60.2144280.9860.9970.0780.2251.11199.9
3.14-3.597.90.13644850.9940.9990.0490.1451.08799.9
3.59-4.528.60.08244670.99810.0280.0861.058100
2.101-2.13898.40.05544680.99910.0180.0581.06799.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.10109691906→36.5246214046 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97789050728 / Phase error: 47.4928584745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245340191267 4014 4.61724276758 %
Rwork0.220575363238 82921 -
obs0.242877936787 86935 97.2318532603 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.8692234347 Å2
Refinement stepCycle: LAST / Resolution: 2.10109691906→36.5246214046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5771 0 0 172 5943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007018648038885852
X-RAY DIFFRACTIONf_angle_d0.9878794249567899
X-RAY DIFFRACTIONf_chiral_restr0.0482448409721894
X-RAY DIFFRACTIONf_plane_restr0.005944634643641042
X-RAY DIFFRACTIONf_dihedral_angle_d27.08661903692242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1027-2.13890.3895491315671750.3539971056013720X-RAY DIFFRACTION81.9383259912
2.1389-2.17780.3619457920291750.3380219826213953X-RAY DIFFRACTION89.5559583145
2.1778-2.21970.3335698612122020.3016624059984157X-RAY DIFFRACTION91.9690265487
2.2197-2.2650.324722171541900.3059857233414105X-RAY DIFFRACTION91.7933810376
2.265-2.31420.3463588363581930.2898735479994112X-RAY DIFFRACTION93.497044111
2.3142-2.3680.349398396182070.2777156423914190X-RAY DIFFRACTION93.1939501779
2.368-2.42720.3161021788812030.272322166824167X-RAY DIFFRACTION93.1797853309
2.4272-2.49280.2924077681742160.2704385486984093X-RAY DIFFRACTION92.3927765237
2.4928-2.56610.2656062125961900.259241718164123X-RAY DIFFRACTION93.5344827586
2.5661-2.64880.2871573633141880.2516502362724231X-RAY DIFFRACTION94.2736185383
2.6488-2.74340.2737565165521980.2420314260834128X-RAY DIFFRACTION93.9035486806
2.7434-2.85320.2339379928061980.2463440303274252X-RAY DIFFRACTION93.7389770723
2.8532-2.98290.2475981486972000.2333986299544185X-RAY DIFFRACTION94.5976491863
2.9829-3.13990.3108252662821960.2336926430144189X-RAY DIFFRACTION94.3893645786
3.1399-3.33630.2079800802182080.2294510752564241X-RAY DIFFRACTION93.4964726631
3.3363-3.59340.2383713060012040.2249062425624177X-RAY DIFFRACTION94.5022624434
3.5934-3.95410.2966651197641960.2061095399264197X-RAY DIFFRACTION94.9118046133
3.9541-4.5240.2020694625392110.1996468924374239X-RAY DIFFRACTION94.7474295932
4.524-5.69140.2251486365651910.1973804200494216X-RAY DIFFRACTION94.8694869487
5.6914-27.39580.2542080331031980.2278666816474196X-RAY DIFFRACTION93.6189201249

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