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- PDB-4tlv: CARDS TOXIN, NICKED -

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Basic information

Entry
Database: PDB / ID: 4tlv
TitleCARDS TOXIN, NICKED
ComponentsADP-ribosylating toxin CARDS
KeywordsTOXIN / TRANSFERASE / MYCOPLASMA PNEUMONIAE / VIRULENCE / ATYPICAL PNEUMONIA / COMMUNITY ACQUIRED RESPIRATORY DISTRESS SYNDROME / ADP-RIBOSYL TRANSFERASE
Function / homology
Function and homology information


symbiont-mediated perturbation of host vacuole organization / attachment organelle / host cell cytosol / host cell endoplasmic reticulum / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / cell projection / toxin activity / lipid binding ...symbiont-mediated perturbation of host vacuole organization / attachment organelle / host cell cytosol / host cell endoplasmic reticulum / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / cell projection / toxin activity / lipid binding / cell surface / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
: / : / ADP-ribosylating toxin CARDS, C-terminal beta-trefoil domain / CARDS D2, beta trefoil domain / Bordetella pertussis toxin A / Pertussis toxin, subunit 1
Similarity search - Domain/homology
ACETATE ION / ADP-ribosylating toxin CARDS
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å
AuthorsTaylor, A.B. / Pakhomova, O.N. / Hart, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of CARDS toxin, a unique ADP-ribosylating and vacuolating cytotoxin from Mycoplasma pneumoniae.
Authors: Becker, A. / Kannan, T.R. / Taylor, A.B. / Pakhomova, O.N. / Zhang, Y. / Somarajan, S.R. / Galaleldeen, A. / Holloway, S.P. / Baseman, J.B. / Hart, P.J.
History
DepositionMay 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylating toxin CARDS
B: ADP-ribosylating toxin CARDS
C: ADP-ribosylating toxin CARDS
D: ADP-ribosylating toxin CARDS
E: ADP-ribosylating toxin CARDS
F: ADP-ribosylating toxin CARDS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,59842
Polymers408,3956
Non-polymers3,20336
Water32,5711808
1
A: ADP-ribosylating toxin CARDS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7449
Polymers68,0661
Non-polymers6798
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylating toxin CARDS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4385
Polymers68,0661
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADP-ribosylating toxin CARDS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7118
Polymers68,0661
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADP-ribosylating toxin CARDS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7749
Polymers68,0661
Non-polymers7088
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ADP-ribosylating toxin CARDS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5897
Polymers68,0661
Non-polymers5236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ADP-ribosylating toxin CARDS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3424
Polymers68,0661
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.698, 107.407, 222.261
Angle α, β, γ (deg.)90.00, 90.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ADP-ribosylating toxin CARDS / ADP-ribosyltransferase CARDS / CARDX TX


Mass: 68065.906 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Strain: ATCC 29342 / M129 / Gene: MPN_372, MP464 / Plasmid: PKA8H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P75409, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1808 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe CARDS toxin was treated with trypsin protease prior to crystallization, leaving a nicked ...The CARDS toxin was treated with trypsin protease prior to crystallization, leaving a nicked polypeptide with non-covalently associated domains defined by residues 1-305 and 308-591. The related un-nicked CARDS toxin in PDB entry 4TLW superimposes on each monomer of this entry with a RMSD of less than 0.4 Angstroms using alpha carbon positions.
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.6 M AMMONIUM SULFATE, 0.08 M SODIUM ACETATE, 20% GLYCEROL
PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 350417 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.073 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.577 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.9→38.87 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 17675 5.05 %
Rwork0.186 --
obs0.188 350157 99.4 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.1115 Å20 Å2-0.6305 Å2
2--2.4738 Å20 Å2
3----5.582 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28352 0 203 1808 30363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129401
X-RAY DIFFRACTIONf_angle_d1.09939975
X-RAY DIFFRACTIONf_dihedral_angle_d13.61710591
X-RAY DIFFRACTIONf_chiral_restr0.0764190
X-RAY DIFFRACTIONf_plane_restr0.0045197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9033-1.92490.28995310.250810407X-RAY DIFFRACTION93
1.9249-1.94750.25855700.235311065X-RAY DIFFRACTION100
1.9475-1.97130.26715490.232411107X-RAY DIFFRACTION100
1.9713-1.99620.27465640.229111189X-RAY DIFFRACTION100
1.9962-2.02250.26296330.226510984X-RAY DIFFRACTION100
2.0225-2.05020.25966320.222710984X-RAY DIFFRACTION100
2.0502-2.07950.24835990.214611137X-RAY DIFFRACTION100
2.0795-2.11050.24856040.209511160X-RAY DIFFRACTION100
2.1105-2.14350.24926470.205510982X-RAY DIFFRACTION100
2.1435-2.17860.24615980.204911074X-RAY DIFFRACTION100
2.1786-2.21620.24015980.201711026X-RAY DIFFRACTION100
2.2162-2.25650.25285650.194911185X-RAY DIFFRACTION100
2.2565-2.29990.23545780.198711127X-RAY DIFFRACTION100
2.2999-2.34680.246040.194611079X-RAY DIFFRACTION100
2.3468-2.39790.22515960.183211188X-RAY DIFFRACTION100
2.3979-2.45360.24175650.195311078X-RAY DIFFRACTION100
2.4536-2.5150.24485850.200711077X-RAY DIFFRACTION100
2.515-2.5830.22636050.193311083X-RAY DIFFRACTION100
2.583-2.6590.23045890.200611140X-RAY DIFFRACTION100
2.659-2.74480.24915860.210311152X-RAY DIFFRACTION100
2.7448-2.84280.23426390.203111039X-RAY DIFFRACTION100
2.8428-2.95660.22166160.198611078X-RAY DIFFRACTION100
2.9566-3.09110.23555350.189211166X-RAY DIFFRACTION100
3.0911-3.2540.20925730.182911105X-RAY DIFFRACTION99
3.254-3.45780.20325950.180411094X-RAY DIFFRACTION99
3.4578-3.72460.19175990.166311071X-RAY DIFFRACTION99
3.7246-4.0990.17615730.152711179X-RAY DIFFRACTION99
4.099-4.69130.14915630.141511098X-RAY DIFFRACTION99
4.6913-5.90720.1815890.158811175X-RAY DIFFRACTION99
5.9072-38.87940.19875950.191111253X-RAY DIFFRACTION98

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