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- PDB-5xnw: Crystal structure of ExoY, a unique nucleotidyl cyclase toxin fro... -

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Basic information

Entry
Database: PDB / ID: 5xnw
TitleCrystal structure of ExoY, a unique nucleotidyl cyclase toxin from Pseudomonas aeruginosa
ComponentsAdenylate cyclase ExoY
KeywordsLYASE / nucleotidyl cyclase / virulence effectors / type three secretion system (T3SS) / secondary messengers
Function / homologyAnthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / calcium- and calmodulin-responsive adenylate cyclase activity / extracellular region / Adenylate cyclase ExoY
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsKhanppnavar, B. / Datta, S.
Funding support India, 2items
OrganizationGrant numberCountry
India
India
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Crystal structure and substrate specificity of ExoY, a unique T3SS mediated secreted nucleotidyl cyclase toxin from Pseudomonas aeruginosa
Authors: Khanppnavar, B. / Datta, S.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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: Adenylate cyclase ExoY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0674
Polymers41,7871
Non-polymers2803
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-14 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.621, 92.621, 66.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Adenylate cyclase ExoY


Mass: 41787.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: exoY, PA2191 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I1S4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.69 Å3/Da / Density % sol: 27.38 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295.15 K / Method: vapor diffusion / pH: 7.5 / Details: 1.5M Lithium Sulphate, 0.1M HEPES / PH range: 7.0-7.8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97885 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 26721 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.035 / Rrim(I) all: 0.107 / Χ2: 1.065 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.248.70.8720.7930.310.9270.866100
2.24-2.288.80.8010.8840.2830.8510.874100
2.28-2.329.20.610.9180.2120.6470.949100
2.32-2.379.20.5610.9220.1940.5940.863100
2.37-2.429.30.5210.9340.1790.5510.949100
2.42-2.489.40.4870.9480.1660.5150.978100
2.48-2.549.40.4080.9610.1390.4311.002100
2.54-2.619.70.350.9680.1180.370.979100
2.61-2.699.70.3050.9740.1020.3220.843100
2.69-2.779.70.2490.9830.0840.2630.875100
2.77-2.879.80.180.9870.060.190.801100
2.87-2.999.70.1660.990.0560.1750.908100
2.99-3.129.70.1290.9920.0430.1360.886100
3.12-3.299.70.1020.9940.0340.1080.812100
3.29-3.499.60.0860.9940.0290.0910.814100
3.49-3.769.60.0840.9930.0290.0890.988100
3.76-4.149.50.0850.990.0290.091.212100
4.14-4.749.40.0690.9940.0230.0730.941100
4.74-5.979.30.0420.9980.0140.0440.39100
5.97-508.40.040.9940.0150.0434.38399.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-20002000data scaling
HKL-2000data reduction
MR-Rosettaphasing
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K8T

1k8t


Resolution: 2.201→46.496 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.76
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2283 2652 9.92 %
Rwork0.1898 --
obs0.1937 26721 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.201→46.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 17 125 2254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022179
X-RAY DIFFRACTIONf_angle_d0.4312937
X-RAY DIFFRACTIONf_dihedral_angle_d17.4851314
X-RAY DIFFRACTIONf_chiral_restr0.039320
X-RAY DIFFRACTIONf_plane_restr0.003388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2006-2.24060.3538970.251854X-RAY DIFFRACTION65
2.2406-2.28370.30341130.2421981X-RAY DIFFRACTION76
2.2837-2.33030.29691240.22281179X-RAY DIFFRACTION88
2.3303-2.3810.27831430.23351273X-RAY DIFFRACTION96
2.381-2.43640.24561470.2241316X-RAY DIFFRACTION100
2.4364-2.49730.2391450.21711315X-RAY DIFFRACTION100
2.4973-2.56480.32951440.21671314X-RAY DIFFRACTION100
2.5648-2.64030.24221450.21731347X-RAY DIFFRACTION100
2.6403-2.72550.2351460.20951303X-RAY DIFFRACTION100
2.7255-2.82290.23371460.18961310X-RAY DIFFRACTION100
2.8229-2.93590.23721440.19121315X-RAY DIFFRACTION100
2.9359-3.06950.25481490.19641322X-RAY DIFFRACTION100
3.0695-3.23130.28841450.18891312X-RAY DIFFRACTION100
3.2313-3.43370.19831450.1771326X-RAY DIFFRACTION100
3.4337-3.69870.21141490.16121318X-RAY DIFFRACTION100
3.6987-4.07070.18091410.15671314X-RAY DIFFRACTION100
4.0707-4.65930.16251430.14171329X-RAY DIFFRACTION100
4.6593-5.86840.21511470.18411322X-RAY DIFFRACTION100
5.8684-46.50680.24811390.22191319X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 20.0456 Å / Origin y: 65.2879 Å / Origin z: 29.5762 Å
111213212223313233
T0.2114 Å2-0.0207 Å20.0153 Å2-0.2877 Å2-0.0349 Å2--0.2013 Å2
L1.4946 °21.2688 °2-0.0342 °2-3.1796 °2-0.1943 °2--1.6666 °2
S-0.0016 Å °0.094 Å °-0.0502 Å °0.2703 Å °0.16 Å °-0.3632 Å °-0.2597 Å °0.3122 Å °-0.1214 Å °
Refinement TLS groupSelection details: all

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