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- PDB-6zc1: Crystal structure of RahU protein from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6zc1
TitleCrystal structure of RahU protein from Pseudomonas aeruginosa
ComponentsRahU protein
KeywordsTOXIN / Aegerolysin / Pseudomonas aeruginosa / RahU protein / protein-membrane interaction
Function / homologyHemolysin, aegerolysin type / Aegerolysin / hemolysis by symbiont of host erythrocytes / glycolipid binding / Aegerolysin
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.27 Å
AuthorsPodobnik, M. / Anderluh, G. / Lenarcic, T.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
CitationJournal: Sci Rep / Year: 2021
Title: Crystal structure of RahU, an aegerolysin protein from the human pathogen Pseudomonas aeruginosa, and its interaction with membrane ceramide phosphorylethanolamine.
Authors: Kocar, E. / Lenarcic, T. / Hodnik, V. / Panevska, A. / Huang, Y. / Bajc, G. / Kostanjsek, R. / Naren, A.P. / Macek, P. / Anderluh, G. / Sepcic, K. / Podobnik, M. / Butala, M.
History
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: RahU protein


Theoretical massNumber of molelcules
Total (without water)15,2561
Polymers15,2561
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.137, 47.939, 40.649
Angle α, β, γ (deg.)90.000, 110.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein RahU protein /


Mass: 15255.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0122 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I710
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: di-Sodium tartrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 16, 2015
Details: a vertical collimating mirror, a double-crystal Si(111) monochromator, a bendable focussing mirror
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→30.87 Å / Num. obs: 39465 / % possible obs: 93.6 % / Redundancy: 6.479 % / Biso Wilson estimate: 12.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.104 / Χ2: 0.973 / Net I/σ(I): 11.8 / Num. measured all: 255698
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.27-1.344.9870.5892.4725358676950850.8090.65875.1
1.34-1.446.6640.4124.3139050637258600.9480.44692
1.44-1.556.7450.2676.7238797592657520.9780.28997.1
1.55-1.76.590.1729.8135406549753730.9880.18697.7
1.7-1.96.9940.11514.1533954493048550.9920.12498.5
1.9-2.196.5310.09218.5428383439543460.9920.198.9
2.19-2.686.7180.08421.1524764372136860.9930.09199.1
2.68-3.796.6290.07823.6818991288828650.9940.08599.2
3.79-30.876.6950.07125.2410994165616420.9930.07799.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.27 Å34.64 Å
Translation1.27 Å34.64 Å

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Processing

Software
NameVersionClassification
XSCALEJan 26, 2018data scaling
PHASER2.7.16phasing
PHENIX1.11.1refinement
PDB_EXTRACT3.24data extraction
XDSJan 26, 2018data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OEB

4oeb


Resolution: 1.27→30.87 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 2000 5.07 %
Rwork0.1591 37461 -
obs0.1595 39461 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.38 Å2 / Biso mean: 16.9725 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: final / Resolution: 1.27→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 0 226 1260
Biso mean---29.98 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041088
X-RAY DIFFRACTIONf_angle_d0.7331489
X-RAY DIFFRACTIONf_chiral_restr0.077161
X-RAY DIFFRACTIONf_plane_restr0.004193
X-RAY DIFFRACTIONf_dihedral_angle_d8.044583
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.27-1.30170.2957990.3525185666
1.3017-1.33690.29941260.2755237383
1.3369-1.37630.22751340.2051249289
1.3763-1.42070.1921420.174266393
1.4207-1.47150.18611450.1738272996
1.4715-1.53040.17781470.16274097
1.5304-1.60.15921490.1588279398
1.6-1.68440.16921480.1468277798
1.6844-1.78990.16451490.1522280098
1.7899-1.92810.17271520.1592283199
1.9281-2.12210.17471490.1522279499
2.1221-2.4290.181520.1589283899
2.429-3.05990.17481520.1632853100
3.0599-30.870.1261560.1373292299
Refinement TLS params.Method: refined / Origin x: 25.1309 Å / Origin y: 36.6105 Å / Origin z: 25.77 Å
111213212223313233
T0.0844 Å2-0.0031 Å20.0029 Å2-0.091 Å20.0071 Å2--0.0836 Å2
L0.9703 °20.1768 °20.1739 °2-0.8044 °20.137 °2--0.718 °2
S0.0377 Å °-0.0111 Å °-0.093 Å °0.067 Å °-0.0146 Å °0.0373 Å °0.0415 Å °-0.0171 Å °0.002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 138
2X-RAY DIFFRACTION1allS1 - 258
3X-RAY DIFFRACTION1allS262 - 267

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