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- PDB-3bw8: Crystal structure of the Clostridium limosum C3 exoenzyme -

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Basic information

Entry
Database: PDB / ID: 3bw8
TitleCrystal structure of the Clostridium limosum C3 exoenzyme
ComponentsMono-ADP-ribosyltransferase C3
KeywordsTRANSFERASE / C3LIM / EXOENZYME C3 / ADP-RIBOSYLTRANSFERASE / RHO / RIBOSYLATING TOXIN / ARTT / C3BOT / C3CER / C3STAU / Glycosyltransferase / NAD / Secreted
Function / homology
Function and homology information


: / pentosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / : / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Mono-ADP-ribosyltransferase C3
Similarity search - Component
Biological speciesClostridium limosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsVogelsgesang, M. / Stieglitz, B. / Herrmann, C. / Pautsch, A. / Aktories, K.
CitationJournal: Febs Lett. / Year: 2008
Title: Crystal structure of the Clostridium limosum C3 exoenzyme.
Authors: Vogelsgesang, M. / Stieglitz, B. / Herrmann, C. / Pautsch, A. / Aktories, K.
History
DepositionJan 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mono-ADP-ribosyltransferase C3
B: Mono-ADP-ribosyltransferase C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9143
Polymers47,8182
Non-polymers961
Water3,945219
1
A: Mono-ADP-ribosyltransferase C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0052
Polymers23,9091
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mono-ADP-ribosyltransferase C3


Theoretical massNumber of molelcules
Total (without water)23,9091
Polymers23,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 91.540, 70.850
Angle α, β, γ (deg.)90.00, 106.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23909.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium limosum (bacteria) / Gene: c3 / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q46134, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG 8000, 200 MM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 7, 2004
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 77583 / Num. obs: 43029 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.22 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.11
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / % possible all: 72.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
TNTrefinement
PDB_EXTRACT3.004data extraction
XDSdata scaling
XDSdata reduction
BUSTER-TNT2.1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G24

1g24


Resolution: 1.8→11.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 2049 5 %RANDOM
Rwork0.195 ---
obs0.1969 40980 90.52 %-
all-40980 --
Displacement parametersBiso mean: 28.39 Å2
Baniso -1Baniso -2Baniso -3
1--12.5433423 Å20 Å2-4.08622135 Å2
2--6.5297146 Å20 Å2
3---6.0136277 Å2
Refinement stepCycle: LAST / Resolution: 1.8→11.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 5 219 3439
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0132772
X-RAY DIFFRACTIONt_angle_deg1.19643972
X-RAY DIFFRACTIONt_dihedral_angle_d19.1766710
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011892
X-RAY DIFFRACTIONt_gen_planes0.0184665
X-RAY DIFFRACTIONt_it1.733327720
X-RAY DIFFRACTIONt_nbd0.038345
LS refinement shellResolution: 1.8→1.91 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2758 270 4.99 %
Rwork0.2274 5139 -
all0.2298 5409 -
obs--90.52 %

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