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- PDB-1r4b: ADP-ribosyltransferase C3bot2 from Clostridium botulinum, monocli... -

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Basic information

Entry
Database: PDB / ID: 1r4b
TitleADP-ribosyltransferase C3bot2 from Clostridium botulinum, monoclinic form
ComponentsMono-ADP-ribosyltransferase C3
KeywordsTRANSFERASE / ADP-RIBOSYLTRANSFERASE / BINARY TOXIN / C3 EXOENZYME
Function / homology
Function and homology information


NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / extracellular region
Similarity search - Function
Mono-ADP-ribosyltransferase C3/Edin / 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
Mono-ADP-ribosyltransferase C3
Similarity search - Component
Biological speciesClostridium phage c-st (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L. / Narumiya, S.
CitationJournal: To be Published
Title: Crystal Structure of ADP-RIBOSYLTRANSFERASE C3bot2 from CLOSTRIDIUM BOTULINUM
Authors: Teplyakov, A. / Obmolova, G. / Gilliland, G.L. / Narumiya, S.
History
DepositionOct 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 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: Mono-ADP-ribosyltransferase C3
B: Mono-ADP-ribosyltransferase C3


Theoretical massNumber of molelcules
Total (without water)46,4512
Polymers46,4512
Non-polymers00
Water4,630257
1
A: Mono-ADP-ribosyltransferase C3


Theoretical massNumber of molelcules
Total (without water)23,2261
Polymers23,2261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono-ADP-ribosyltransferase C3


Theoretical massNumber of molelcules
Total (without water)23,2261
Polymers23,2261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.300, 70.000, 109.000
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mono-ADP-ribosyltransferase C3 / Exoenzyme C3


Mass: 23225.521 Da / Num. of mol.: 2 / Fragment: mature protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phage c-st (virus) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q00901, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Lithium Sulfate, 7% PEG 4000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 1996 / Details: mirror
RadiationMonochromator: Germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 35373 / Num. obs: 35373 / % possible obs: 85 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.058
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.235 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G24

1g24


Resolution: 1.85→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.88 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1416 4 %RANDOM
Rwork0.163 ---
all0.164 33725 --
obs0.164 33725 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20.16 Å2
2--0.59 Å20 Å2
3----0.99 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 0 257 3471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223282
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9644413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9745398
X-RAY DIFFRACTIONr_chiral_restr0.0950.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022478
X-RAY DIFFRACTIONr_nbd_refined0.2360.21347
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3860.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.27
X-RAY DIFFRACTIONr_mcbond_it3.71831992
X-RAY DIFFRACTIONr_mcangle_it5.79963223
X-RAY DIFFRACTIONr_scbond_it8.28381290
X-RAY DIFFRACTIONr_scangle_it11.76681190
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 68
Rwork0.225 1530

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