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- PDB-6in9: Crystal structure of MucB in complex with MucA(peri) -

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Basic information

Entry
Database: PDB / ID: 6in9
TitleCrystal structure of MucB in complex with MucA(peri)
Components
  • Sigma factor AlgU negative regulatory protein
  • Sigma factor AlgU regulatory protein MucB
KeywordsMEMBRANE PROTEIN / Outer membrane protein
Function / homology
Function and homology information


regulation of polysaccharide biosynthetic process / antisigma factor binding / alginic acid biosynthetic process / sigma factor antagonist activity / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / MucB/RseB / MucB/RseB, N-terminal / MucB/RseB, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / MucB/RseB, C-terminal domain superfamily / : / Anti sigma-E protein RseA, N-terminal domain / Anti sigma-E protein RseA, C-terminal domain ...Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / MucB/RseB / MucB/RseB, N-terminal / MucB/RseB, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / MucB/RseB, C-terminal domain superfamily / : / Anti sigma-E protein RseA, N-terminal domain / Anti sigma-E protein RseA, C-terminal domain / MucB/RseB N-terminal domain / MucB/RseB C-terminal domain
Similarity search - Domain/homology
Sigma factor AlgU negative regulatory protein / Sigma factor AlgU regulatory protein MucB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sigma factor AlgU regulatory protein MucB
B: Sigma factor AlgU regulatory protein MucB
C: Sigma factor AlgU negative regulatory protein
D: Sigma factor AlgU negative regulatory protein


Theoretical massNumber of molelcules
Total (without water)84,3064
Polymers84,3064
Non-polymers00
Water7,584421
1
A: Sigma factor AlgU regulatory protein MucB
D: Sigma factor AlgU negative regulatory protein


Theoretical massNumber of molelcules
Total (without water)42,1532
Polymers42,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-16 kcal/mol
Surface area14580 Å2
MethodPISA
2
B: Sigma factor AlgU regulatory protein MucB
C: Sigma factor AlgU negative regulatory protein


Theoretical massNumber of molelcules
Total (without water)42,1532
Polymers42,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-17 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.149, 50.268, 100.137
Angle α, β, γ (deg.)90.00, 109.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sigma factor AlgU regulatory protein MucB / MucB


Mass: 32440.434 Da / Num. of mol.: 2
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: mucB, algN, PA0764 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P38108
#2: Protein Sigma factor AlgU negative regulatory protein / MucA


Mass: 9712.626 Da / Num. of mol.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium citrate tribasic monohydrate, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 61207 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rpim(I) all: 0.044 / Net I/σ(I): 17.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3024 / Rpim(I) all: 0.262

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P4B

2p4b


Resolution: 1.801→44.396 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.22
RfactorNum. reflection% reflection
Rfree0.2162 3039 4.97 %
Rwork0.1879 --
obs0.1893 61170 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→44.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 0 421 5305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094991
X-RAY DIFFRACTIONf_angle_d1.0926776
X-RAY DIFFRACTIONf_dihedral_angle_d21.1922999
X-RAY DIFFRACTIONf_chiral_restr0.061757
X-RAY DIFFRACTIONf_plane_restr0.006897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8013-1.82940.30081130.25192552X-RAY DIFFRACTION97
1.8294-1.85940.28711000.24232678X-RAY DIFFRACTION100
1.8594-1.89150.27841610.22492600X-RAY DIFFRACTION99
1.8915-1.92590.22921280.20532608X-RAY DIFFRACTION100
1.9259-1.96290.2551460.19662616X-RAY DIFFRACTION100
1.9629-2.0030.22591460.19552652X-RAY DIFFRACTION100
2.003-2.04660.23311370.19322578X-RAY DIFFRACTION100
2.0466-2.09420.22291420.18912620X-RAY DIFFRACTION99
2.0942-2.14650.23841200.18722664X-RAY DIFFRACTION100
2.1465-2.20460.19931230.1872658X-RAY DIFFRACTION100
2.2046-2.26940.21981390.18112643X-RAY DIFFRACTION100
2.2694-2.34270.21771320.18932619X-RAY DIFFRACTION100
2.3427-2.42640.23791530.19552626X-RAY DIFFRACTION100
2.4264-2.52350.26311420.19412635X-RAY DIFFRACTION100
2.5235-2.63840.26441510.2022642X-RAY DIFFRACTION100
2.6384-2.77750.22381510.20072640X-RAY DIFFRACTION100
2.7775-2.95140.21521510.19612652X-RAY DIFFRACTION100
2.9514-3.17930.22111300.19162677X-RAY DIFFRACTION100
3.1793-3.49910.19311290.17662678X-RAY DIFFRACTION100
3.4991-4.00510.19171590.17092640X-RAY DIFFRACTION100
4.0051-5.04490.16251480.15562702X-RAY DIFFRACTION100
5.0449-44.40930.23791380.20512751X-RAY DIFFRACTION99

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