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- PDB-6sus: Crystal structure of RTX domain blocks IV and V of adenylate cycl... -

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Basic information

Entry
Database: PDB / ID: 6sus
TitleCrystal structure of RTX domain blocks IV and V of adenylate cyclase toxin from Bordetella pertussis
ComponentsBifunctional hemolysin/adenylate cyclase
KeywordsTOXIN / ADENYLATE CYCLASE / RTX MOTIFS / CALCIUM BINDING
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding / calcium ion binding ...calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / calmodulin binding / calcium ion binding / host cell plasma membrane / extracellular region / ATP binding / membrane
Similarity search - Function
RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site ...RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
NITRATE ION / TRIETHYLENE GLYCOL / Bifunctional hemolysin/adenylate cyclase
Similarity search - Component
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsMotlova, L. / Barinka, C. / Bumba, L.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Continuous Assembly of beta-Roll Structures Is Implicated in the Type I-Dependent Secretion of Large Repeat-in-Toxins (RTX) Proteins.
Authors: Motlova, L. / Klimova, N. / Fiser, R. / Sebo, P. / Bumba, L.
History
DepositionSep 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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: Bifunctional hemolysin/adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,84824
Polymers32,5141
Non-polymers1,33423
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-35 kcal/mol
Surface area12370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.771, 91.771, 104.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional hemolysin/adenylate cyclase / AC-HLY / ACT / Cyclolysin


Mass: 32513.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Gene: cya, cyaA, BP0760
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DKX7, adenylate cyclase

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Non-polymers , 6 types, 200 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.14 Å3/Da / Density % sol: 70.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NH4NO3 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 44820 / % possible obs: 99.8 % / Redundancy: 8.94 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.055 / Net I/σ(I): 24.66
Reflection shellResolution: 1.76→1.87 Å / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 7085 / CC1/2: 0.858 / Rrim(I) all: 0.881 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CVW

5cvw


Resolution: 1.76→45.89 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.082
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 2100 4.7 %RANDOM
Rwork0.1836 ---
obs0.1844 42719 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.24 Å2 / Biso mean: 35.519 Å2 / Biso min: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.76→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 63 177 2111
Biso mean--43.33 43.32 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0162087
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181776
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.7512828
X-RAY DIFFRACTIONr_angle_other_deg3.9781.8764160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93923.393112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57515276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2611513
X-RAY DIFFRACTIONr_chiral_restr0.0530.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022578
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02390
X-RAY DIFFRACTIONr_mcbond_it2.2833.4231114
X-RAY DIFFRACTIONr_mcbond_other2.2823.4281115
X-RAY DIFFRACTIONr_mcangle_it3.2135.1021414
LS refinement shellResolution: 1.76→1.81 Å
RfactorNum. reflection% reflection
Rfree0.273 151 -
Rwork0.262 3075 -
obs--98.87 %

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