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- PDB-5wft: PelB 319-436 from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 5wft
TitlePelB 319-436 from Pseudomonas aeruginosa PAO1
ComponentsPelB
KeywordsSTRUCTURAL PROTEIN / Tetratricopeptide repeat
Function / homologyextracellular polysaccharide biosynthetic process / single-species biofilm formation / Tetratricopeptide-like helical domain superfamily / membrane => GO:0016020 / PelB
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.821 Å
AuthorsMarmont, L.S. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: PelA and PelB proteins form a modification and secretion complex essential for Pel polysaccharide-dependent biofilm formation in Pseudomonas aeruginosa.
Authors: Marmont, L.S. / Whitfield, G.B. / Rich, J.D. / Yip, P. / Giesbrecht, L.B. / Stremick, C.A. / Whitney, J.C. / Parsek, M.R. / Harrison, J.J. / Howell, P.L.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PelB


Theoretical massNumber of molelcules
Total (without water)13,7401
Polymers13,7401
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.140, 61.140, 217.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PelB


Mass: 13740.042 Da / Num. of mol.: 1 / Fragment: UNP residues 319-436
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: pelB, PA3063 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZE5

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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: 4.28 Å3/Da / Density % sol: 71.23 % / Description: hexagonal bipyramid
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 HEPES pH 7.5, 13% (w/v) PEG 3350, 0.2 M proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 10961 / % possible obs: 99.8 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.821→42.776 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 22.81
RfactorNum. reflection% reflection
Rfree0.2718 640 10 %
Rwork0.2154 --
obs0.2208 6401 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.821→42.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 0 0 945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008968
X-RAY DIFFRACTIONf_angle_d1.0941315
X-RAY DIFFRACTIONf_dihedral_angle_d17.193570
X-RAY DIFFRACTIONf_chiral_restr0.055138
X-RAY DIFFRACTIONf_plane_restr0.007173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8205-3.03830.3491230.27091108X-RAY DIFFRACTION100
3.0383-3.34390.26971230.23881109X-RAY DIFFRACTION100
3.3439-3.82750.29431260.22891132X-RAY DIFFRACTION100
3.8275-4.82120.21121280.17681150X-RAY DIFFRACTION100
4.8212-42.78130.271400.20171262X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1714-0.1806-0.48451.25-0.01532.0119-0.0013-0.0053-0.09210.06840.0520.22420.0919-0.2359-0.03190.1293-0.04910.0870.21080.04030.145510.4654-18.5006-132.5917
22.4989-0.1887-0.61410.9450.3161.89020.1754-0.13680.34430.044-0.00190.0806-0.2764-0.227-0.17240.1914-0.00510.14390.23640.02450.18247.7635-15.9934-121.5579
33.37770.1899-2.11971.13680.26783.06130.16-0.3984-0.01680.2323-0.1020.0259-0.2040.1437-0.06320.1739-0.1120.07350.3264-0.01390.18993.1256-19.5433-106.999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 319 through 350 )
2X-RAY DIFFRACTION2chain 'A' and (resid 351 through 387 )
3X-RAY DIFFRACTION3chain 'A' and (resid 388 through 436 )

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