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- PDB-1he9: Crystal structure of the GAP domain of the Pseudomonas aeruginosa... -

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Basic information

Entry
Database: PDB / ID: 1he9
TitleCrystal structure of the GAP domain of the Pseudomonas aeruginosa ExoS toxin
ComponentsEXOENZYME S
KeywordsTOXIN (EXOENZYME S) / EXOS / PSEUDOMONAS AERUGINOSA / GAP / TOXIN / VIRULENCE FACTOR / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


glycosyltransferase activity / GTPase activator activity / nucleotidyltransferase activity / toxin activity / extracellular region
Similarity search - Function
Virulence factor YopE uncharacterised domain / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsWurtele, M. / Renault, L. / Barbieri, J.T. / Wittinghofer, A. / Wolf, E.
CitationJournal: FEBS Lett. / Year: 2001
Title: Structure of the Exos Gtpase Activating Domain
Authors: Wurtele, M. / Renault, L. / Barbieri, J.T. / Wittinghofer, A. / Wolf, E.
History
DepositionNov 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXOENZYME S


Theoretical massNumber of molelcules
Total (without water)14,4331
Polymers14,4331
Non-polymers00
Water1,17165
1
A: EXOENZYME S

A: EXOENZYME S


Theoretical massNumber of molelcules
Total (without water)28,8662
Polymers28,8662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area1770 Å2
ΔGint-10.9 kcal/mol
Surface area15420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)42.897, 55.646, 107.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein EXOENZYME S / EXOS


Mass: 14432.834 Da / Num. of mol.: 1 / Fragment: 96-234 GTPASE-ACTIVATING PROTEIN (GAP-DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Gene: EXOS / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q51451
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growpH: 5.5
Details: MGCL2, (NH4)2SO4, PEG 6000, NA-CACODYLATE PH5.5, pH 5.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
225 mMTris1drop
316 %PEG60001reservoir
40.2 Mammonium sulfate1reservoir
510 mM1reservoirMgCl2
6100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9789,0.9790,0.8856,1.54
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.9791
30.88561
41.541
ReflectionResolution: 2.4→20 Å / Num. obs: 5237 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Rsym value: 0.053 / Net I/σ(I): 34
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 8 / Rsym value: 0.175 / % possible all: 98.4
Reflection
*PLUS
% possible obs: 95.3 % / Num. measured all: 68947 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.175

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1274374.44 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FIRST POST SUBMISSION CORRECTION C- TERMINUS NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 518 9.9 %RANDOM
Rwork0.257 ---
obs0.257 5237 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.8674 Å2 / ksol: 0.389157 e/Å3
Displacement parametersBiso mean: 62.4 Å2
Baniso -1Baniso -2Baniso -3
1--13.82 Å20 Å20 Å2
2--28.18 Å20 Å2
3----14.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 0 65 1065
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.36
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.961.5
X-RAY DIFFRACTIONc_mcangle_it3.442
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it4.142.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 85 10.2 %
Rwork0.311 747 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.36

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