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- PDB-2wn4: Structural Basis for Substrate Recognition in the Enzymatic Compo... -

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Basic information

Entry
Database: PDB / ID: 2wn4
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


Transferases; Glycosyltransferases; Pentosyltransferases / 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: 1.85 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.901, 44.523, 78.038
Angle α, β, γ (deg.)90.00, 102.84, 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 CODON PLUS (DE3)-RIPL / References: UniProt: Q9KH42
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2M K-THIOCYANATE, 0.1 M TRIS PH 8.5, 20% PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 17, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 33361 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.12
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.86 / % possible all: 76.3

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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: 1.85→38.04 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.274 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23906 1628 5.1 %RANDOM
Rwork0.19974 ---
obs0.20176 30395 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.551 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 0 424 3531
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_deg0.9421.9694332
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3375395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14725.135148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61615579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0421514
X-RAY DIFFRACTIONr_chiral_restr0.0630.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212426
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_it0.3831.51970
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74623189
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07331233
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8484.51143
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: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 91 -
Rwork0.24 1705 -
obs--74.06 %

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