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- PDB-6jnp: Structure of ExoT-SpcS Complex from Pseudomonas aeruginosa in 2.2... -

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Basic information

Entry
Database: PDB / ID: 6jnp
TitleStructure of ExoT-SpcS Complex from Pseudomonas aeruginosa in 2.2 Angstrom
Components
  • CesT family type III secretion system chaperone
  • Exoenzyme T
KeywordsTOXIN / ExoT / SpcS / T3SS / Pseudomonas / Pseudomonas aeruginosa / chaperone / Effector / Exotoxin / Effector-toxin
Function / homology
Function and homology information


NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / protein secretion by the type III secretion system / : / NAD+-protein poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / GTPase activator activity / toxin activity / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2690 / Type III secretion chaperone SycE / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2690 / Type III secretion chaperone SycE / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Probable chaperone / CesT family type III secretion system chaperone / Exoenzyme T
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.261 Å
AuthorsDatta, S. / Mondal, A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial ResearchTREAT- BSC0113, UNSEEN-BSC0116 India
CitationJournal: To Be Published
Title: Structure of ExoT-SpcS Complex from Pseudomonas aeruginosa
Authors: Datta, S. / Mondal, A.
History
DepositionMar 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Exoenzyme T
B: CesT family type III secretion system chaperone
C: CesT family type III secretion system chaperone
D: Exoenzyme T
E: CesT family type III secretion system chaperone
F: CesT family type III secretion system chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3048
Polymers65,1206
Non-polymers1842
Water2,792155
1
A: Exoenzyme T
B: CesT family type III secretion system chaperone
C: CesT family type III secretion system chaperone
hetero molecules

D: Exoenzyme T
E: CesT family type III secretion system chaperone
F: CesT family type III secretion system chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3048
Polymers65,1206
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area16140 Å2
ΔGint-95 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.000, 63.000, 83.000
Angle α, β, γ (deg.)90.00, 98.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Exoenzyme T


Mass: 6216.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: yopE, NCTC13719_06179 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A379I277, UniProt: Q9I788*PLUS
#2: Protein
CesT family type III secretion system chaperone / YopE regulator


Mass: 13171.843 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: yerA / Production host: Escherichia coli (E. coli) / References: UniProt: Q51450, UniProt: G3XD93*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 295.1 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 25% PEG3350, 0.1 M Bis-Tris pH5.7-6.5 / PH range: 5.7-6.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23043 / % possible obs: 90.28 % / Redundancy: 2.7 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.26 Å / Num. unique obs: 1072 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JMF

4jmf


Resolution: 2.261→34.793 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.13
RfactorNum. reflection% reflection
Rfree0.2535 1839 7.98 %
Rwork0.211 --
obs0.2145 23043 90.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.261→34.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 12 155 4741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024678
X-RAY DIFFRACTIONf_angle_d0.5256350
X-RAY DIFFRACTIONf_dihedral_angle_d15.4572878
X-RAY DIFFRACTIONf_chiral_restr0.036704
X-RAY DIFFRACTIONf_plane_restr0.004858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2614-2.32250.4195880.30831072X-RAY DIFFRACTION59
2.3225-2.39080.32711260.2711458X-RAY DIFFRACTION83
2.3908-2.4680.30441400.28061525X-RAY DIFFRACTION86
2.468-2.55620.32441380.2691583X-RAY DIFFRACTION87
2.5562-2.65850.3371440.26321607X-RAY DIFFRACTION89
2.6585-2.77940.32091380.25631622X-RAY DIFFRACTION91
2.7794-2.92590.29891430.24381677X-RAY DIFFRACTION93
2.9259-3.10910.29011500.24741726X-RAY DIFFRACTION96
3.1091-3.3490.30961500.23071746X-RAY DIFFRACTION96
3.349-3.68560.25971550.19811774X-RAY DIFFRACTION98
3.6856-4.21820.19471550.17461786X-RAY DIFFRACTION99
4.2182-5.31140.18281530.1581808X-RAY DIFFRACTION99
5.3114-34.79680.18721590.17281820X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 5.5288 Å / Origin y: 11.2333 Å / Origin z: 18.5547 Å
111213212223313233
T0.193 Å20.0321 Å2-0.0155 Å2-0.159 Å20.0328 Å2--0.1693 Å2
L0.6332 °20.2863 °2-0.1627 °2-1.0657 °20.416 °2--0.8215 °2
S-0.0073 Å °0.0535 Å °0.0138 Å °0.0475 Å °0.0581 Å °-0.0673 Å °0.0163 Å °0.1118 Å °-0.0555 Å °
Refinement TLS groupSelection details: all

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