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- PDB-6zc2: Crystal structure of RahU protein in complex with TRIS molecule -

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Basic information

Entry
Database: PDB / ID: 6zc2
TitleCrystal structure of RahU protein in complex with TRIS molecule
ComponentsRahU protein
KeywordsTOXIN / Aegerolysin / Pseudomonas aeruginosa / RahU protein / protein-membrane interaction
Function / homologyHemolysin, aegerolysin type / Aegerolysin / hemolysis by symbiont of host erythrocytes / glycolipid binding / Hemolysin
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,93611
Polymers15,2561
Non-polymers68110
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint33 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.338, 48.112, 40.422
Angle α, β, γ (deg.)90.000, 110.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-441-

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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris/HCl pH 8.5, PEG 8000

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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: Jul 30, 2016
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: 1.12→41.463 Å / Num. obs: 59138 / % possible obs: 98.9 % / Redundancy: 3.258 % / Biso Wilson estimate: 9.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Χ2: 0.989 / Net I/σ(I): 17.19 / Num. measured all: 192688
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
1.12-1.193.020.3862.9528083960493000.8990.46896.8
1.19-1.273.2740.2225.2129382903589730.9540.26599.3
1.27-1.373.220.147.9726916842783600.9780.16899.2
1.37-1.53.0990.08512.1123929777677220.990.10399.3
1.5-1.683.4940.05120.0324469704470040.9960.0699.4
1.68-1.943.450.03726.9421312621061780.9980.04399.5
1.94-2.383.1390.02835.4116483528552510.9980.03499.4
2.38-3.363.4310.02543.2313982410940750.9990.02999.2
3.36-41.4633.5750.02349.938132230922750.9990.02798.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.13 Å41.46 Å

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Processing

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

4oeb


Resolution: 1.13→41.463 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1563 1999 3.38 %
Rwork0.1387 57134 -
obs0.1392 59133 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.67 Å2 / Biso mean: 15.9176 Å2 / Biso min: 7.58 Å2
Refinement stepCycle: final / Resolution: 1.13→41.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 44 149 1227
Biso mean--27.47 28.44 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051151
X-RAY DIFFRACTIONf_angle_d0.7561565
X-RAY DIFFRACTIONf_chiral_restr0.078169
X-RAY DIFFRACTIONf_plane_restr0.005199
X-RAY DIFFRACTIONf_dihedral_angle_d13.2609
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.13-1.15830.31811390.2857397598
1.1583-1.18960.21021440.1888410199
1.1896-1.22460.17641420.1666405999
1.2246-1.26420.18571410.1568404999
1.2642-1.30930.15611430.1294406699
1.3093-1.36180.1371420.1272406899
1.3618-1.42380.14871430.1247407099
1.4238-1.49880.14781430.1154407599
1.4988-1.59270.13341420.10914086100
1.5927-1.71570.11831430.1124071100
1.7157-1.88840.11861440.11964117100
1.8884-2.16160.16021440.12974109100
2.1616-2.72330.15531440.1473411499
2.7233-41.4630.17071450.1472417499

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