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- PDB-1gzf: Structure of the Clostridium botulinum C3 exoenzyme (wild-type) i... -

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Basic information

Entry
Database: PDB / ID: 1gzf
TitleStructure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD
ComponentsMONO-ADP-RIBOSYLTRANSFERASE C3
KeywordsTRANSFERASE / ADP-RIBOSYLTRANSFERASE / BACTERIAL TOXIN / C3 EXOENZYME
Function / homology
Function and homology information


NAD+-protein mono-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
ADENOSINE-5'-DIPHOSPHATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NIR / Mono-ADP-ribosyltransferase C3
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.95 Å
AuthorsMenetrey, J. / Flatau, G. / Stura, E.A. / Charbonnier, J.B. / Gas, F. / Teulon, J.M. / Le Du, M.H. / Boquet, P. / Menez, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Nad Binding Induces Conformational Changes in Rho Adp-Ribosylating Clostridium Botulinum C3 Exoenzyme
Authors: Menetrey, J. / Flatau, G. / Stura, E.A. / Charbonnier, J.B. / Gas, F. / Teulon, J.M. / Le Du, M.H. / Boquet, P. / Menez, A.
History
DepositionMay 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

Downloads & links

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Assembly

Deposited unit
A: MONO-ADP-RIBOSYLTRANSFERASE C3
B: MONO-ADP-RIBOSYLTRANSFERASE C3
C: MONO-ADP-RIBOSYLTRANSFERASE C3
D: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,98411
Polymers94,3684
Non-polymers2,6167
Water10,269570
1
A: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3513
Polymers23,5921
Non-polymers7592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3513
Polymers23,5921
Non-polymers7592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2613
Polymers23,5921
Non-polymers6692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0192
Polymers23,5921
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.947, 74.191, 119.680
Angle α, β, γ (deg.)90.00, 102.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
MONO-ADP-RIBOSYLTRANSFERASE C3 / EXOENZYME C3


Mass: 23591.969 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN, RESIDUES 41-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P15879, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 5 types, 577 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NIR / 3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM


Mass: 242.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O4
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.39 Å3/Da / Density % sol: 41.5 %
Crystal growpH: 3
Details: 22.5 % PEG 3350 W/W, 100MM LI2SO4, 80 MM ACID CITRIC PH 3 ADDED WITH 20MM NAD FOR 60MN
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
222.5 %(w/w)PEG33501reservoir
3100 mM1reservoirLi2SO4
480 mMcitric acid1reservoirpH3.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.009
DetectorDate: Mar 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 62950 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 157546
Reflection shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2 Å / % possible obs: 96.2 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.95→25 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Details: DISORDERED N- AND C-TERMINII WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3195 5.1 %RANDOM
Rwork0.234 ---
obs0.234 62950 96.8 %-
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 169 570 7223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.027
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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