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- PDB-2wn8: Structural Basis for Substrate Recognition in the Enzymatic Compo... -

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Basic information

Entry
Database: PDB / ID: 2wn8
TitleStructural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile
ComponentsADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT
KeywordsTRANSFERASE / CDTA / ACTIN-ADPRT / BINARY TOXIN / RIBOSYLTRANSFERASE
Function / homology
Function and homology information


transferase activity / nucleotide binding / extracellular region / metal ion binding
Similarity search - Function
Binary exotoxin A, clostridial type / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADP-ribosyltransferase enzymatic component
Similarity search - Component
Biological speciesCLOSTRIDIUM DIFFICILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSundriyal, A. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Basis for Substrate Recognition in the Enzymatic Component of Adp-Ribosyltransferase Toxin Cdta from Clostridium Difficile.
Authors: Sundriyal, A. / Roberts, A.K. / Shone, C.C. / Acharya, K.R.
History
DepositionJul 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT


Theoretical massNumber of molelcules
Total (without water)53,3231
Polymers53,3231
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.091, 42.744, 77.004
Angle α, β, γ (deg.)90.00, 102.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ADP-RIBOSYLTRANSFERASE ENZYMATIC COMPONENT / ACTIN-RIBOSYLATING TOXIN / CDTA


Mass: 53323.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Plasmid: PMAL-P2X / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) CODON PLUS RIPL / References: UniProt: Q9KH42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.04 Å3/Da / Density % sol: 39.7 % / Description: NONE
Crystal growpH: 4 / Details: 0.1M MIB BUFFER PH 4.0, 20% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.3625
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3625 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24824 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.94 / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GIQ

1giq


Resolution: 2→25.06 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.285 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27957 1201 5.1 %RANDOM
Rwork0.21976 ---
obs0.22286 22120 93.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.392 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 0 154 3291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223203
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.9714323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60825.033151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69915591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0421515
X-RAY DIFFRACTIONr_chiral_restr0.070.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212410
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4471.51942
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85623148
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2631261
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1694.51175
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 68 -
Rwork0.25 1239 -
obs--71.46 %

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