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- PDB-6jau: The complex structure of Pseudomonas aeruginosa MucA/MucB. -

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Basic information

Entry
Database: PDB / ID: 6jau
TitleThe complex structure of Pseudomonas aeruginosa MucA/MucB.
Components(Sigma factor AlgU ...) x 2
KeywordsPROTEIN BINDING / MucA/MucB / Regulated Intramembrane Proteolysis / LPS / Alginate
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 / 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: 1.905 Å
AuthorsLi, T. / He, L.H. / Li, C.C. / Liu, L. / Peng, C.T. / Shen, Y.L. / Qin, X.F. / Xiao, Q.J. / Zhu, Y.B. / Song, Y.J. ...Li, T. / He, L.H. / Li, C.C. / Liu, L. / Peng, C.T. / Shen, Y.L. / Qin, X.F. / Xiao, Q.J. / Zhu, Y.B. / Song, Y.J. / Zhao, N.l. / Zhao, C. / Yang, J. / Mu, X.Y. / Huang, Q. / Bao, R.
CitationJournal: Commun Biol / Year: 2020
Title: Molecular basis of the lipid-induced MucA-MucB dissociation in Pseudomonas aeruginosa.
Authors: Li, T. / He, L. / Li, C. / Kang, M. / Song, Y. / Zhu, Y. / Shen, Y. / Zhao, N. / Zhao, C. / Yang, J. / Huang, Q. / Mou, X. / Tong, A. / Yang, J. / Wang, Z. / Ji, C. / Li, H. / Tang, H. / Bao, R.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sigma factor AlgU regulatory protein MucB
B: Sigma factor AlgU negative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7105
Polymers44,2952
Non-polymers4153
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-32 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.907, 186.429, 50.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

21A-669-

HOH

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Components

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Sigma factor AlgU ... , 2 types, 2 molecules AB

#1: Protein Sigma factor AlgU regulatory protein MucB


Mass: 33511.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain 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) / Strain (production host): BL21(DE3) / References: UniProt: P38108
#2: Protein Sigma factor AlgU negative regulatory protein


Mass: 10783.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PAO1) (bacteria)
Strain: PAO1/ ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101
Gene: mucA, PA0763 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38107

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Non-polymers , 4 types, 189 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.83 Å3/Da / Density % sol: 32.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30%PEG550, 0.1M BIS-TRIS PH 6.5, 0.05M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 26846 / % possible obs: 99.9 % / Redundancy: 10 % / Net I/σ(I): 15.57
Reflection shellResolution: 1.9→1.93 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.905→35.953 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 44.61 / Phase error: 15.57
RfactorNum. reflection% reflection
Rfree0.1929 2000 7.45 %
Rwork0.1729 --
obs0.1744 26846 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.905→35.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 26 186 2782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0282647
X-RAY DIFFRACTIONf_angle_d1.9193587
X-RAY DIFFRACTIONf_dihedral_angle_d16.576976
X-RAY DIFFRACTIONf_chiral_restr0.182396
X-RAY DIFFRACTIONf_plane_restr0.012473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.905-1.95260.21371300.21091623X-RAY DIFFRACTION91
1.9526-2.00540.22441390.20211712X-RAY DIFFRACTION97
2.0054-2.06440.20611380.18921718X-RAY DIFFRACTION98
2.0644-2.13110.22731420.17721769X-RAY DIFFRACTION100
2.1311-2.20720.18121420.16961763X-RAY DIFFRACTION100
2.2072-2.29560.18471430.17371776X-RAY DIFFRACTION100
2.2956-2.40.17071430.1661777X-RAY DIFFRACTION100
2.4-2.52650.20771430.17511771X-RAY DIFFRACTION100
2.5265-2.68480.21981430.18041792X-RAY DIFFRACTION100
2.6848-2.8920.2011440.17821778X-RAY DIFFRACTION100
2.892-3.18290.2021460.17311804X-RAY DIFFRACTION100
3.1829-3.64310.17011450.15341822X-RAY DIFFRACTION100
3.6431-4.58840.15891480.14661826X-RAY DIFFRACTION100
4.5884-35.95990.21091540.18941915X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 52.9371 Å / Origin y: 25.4476 Å / Origin z: 32.2674 Å
111213212223313233
T0.0819 Å20.0103 Å2-0.0015 Å2-0.1015 Å2-0.0097 Å2--0.0914 Å2
L0.5896 °20.4857 °20.3365 °2-0.8106 °20.315 °2--0.4211 °2
S0.0173 Å °0.0036 Å °-0.0327 Å °-0.0565 Å °-0.006 Å °0.0256 Å °0.0106 Å °-0.0613 Å °-0.0125 Å °
Refinement TLS groupSelection details: all

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