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- PDB-1g24: THE CRYSTAL STRUCTURE OF EXOENZYME C3 FROM CLOSTRIDIUM BOTULINUM -

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Basic information

Entry
Database: PDB / ID: 1g24
TitleTHE CRYSTAL STRUCTURE OF EXOENZYME C3 FROM CLOSTRIDIUM BOTULINUM
ComponentsEXOENZYME C3
KeywordsTRANSFERASE / C3 / ADP-ribosyltransferase
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 botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHan, S. / Arvai, A.S. / Clancy, S.B. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.
Authors: Han, S. / Arvai, A.S. / Clancy, S.B. / Tainer, J.A.
History
DepositionOct 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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: EXOENZYME C3
B: EXOENZYME C3
C: EXOENZYME C3
D: EXOENZYME C3


Theoretical massNumber of molelcules
Total (without water)94,3684
Polymers94,3684
Non-polymers00
Water15,655869
1
A: EXOENZYME C3


Theoretical massNumber of molelcules
Total (without water)23,5921
Polymers23,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EXOENZYME C3


Theoretical massNumber of molelcules
Total (without water)23,5921
Polymers23,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: EXOENZYME C3


Theoretical massNumber of molelcules
Total (without water)23,5921
Polymers23,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: EXOENZYME C3


Theoretical massNumber of molelcules
Total (without water)23,5921
Polymers23,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)233.747, 73.757, 73.749
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
EXOENZYME C3 / E.C.2.4.2.- / MONO-ADP-RIBOSYLTRANSFERASE C3


Mass: 23591.969 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 5000, monomethylether, ethyleneglycol, imidazole, malate, sodium orthovanadate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %mPEG50001reservoir
23 %satsodium orthovandate1reservoir
310 %ethylene glycol1reservoir
4100 mMimidazole/malate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: RIGAKU AFC-5 / Detector: CCD / Date: Apr 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 124350 / Num. obs: 124350 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 22 Å2 / Rsym value: 5.7 / Net I/σ(I): 6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 12418 / Rsym value: 16.4
Reflection
*PLUS
% possible obs: 94.6 % / Num. measured all: 359859 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.164

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QS1

1qs1


Resolution: 1.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 12412 11.1 %RANDOM
Rwork0.24 ---
all0.24 124349 --
obs0.24 111937 9.4 %-
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 0 869 7493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.18

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