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- PDB-1uzi: C3 EXOENZYME FROM CLOSTRIDIUM BOTULINUM, TETRAGONAL FORM -

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Basic information

Entry
Database: PDB / ID: 1uzi
TitleC3 EXOENZYME FROM CLOSTRIDIUM BOTULINUM, TETRAGONAL FORM
ComponentsMONO-ADP-RIBOSYLTRANSFERASE 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
CYCLO-TETRAMETAVANADATE / VANADATE ION / Mono-ADP-ribosyltransferase C3
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsEvans, H.R. / Holloway, D.E. / Sutton, J.M. / Ayriss, J. / Shone, C.C. / Acharya, K.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: C3 Exoenzyme from Clostridium Botulinum: Structure of a Tetragonal Crystal Form and a Reassessment of Nad-Induced Flexure
Authors: Evans, H.R. / Holloway, D.E. / Sutton, J.M. / Ayriss, J. / Shone, C.C. / Acharya, K.R.
History
DepositionMar 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

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)48,1098
Polymers47,1842
Non-polymers9256
Water5,549308
1
A: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4026
Polymers23,5921
Non-polymers8105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7072
Polymers23,5921
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.293, 73.293, 218.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-2060-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.000267, -0.000458), (-1, 0.000453), (-0.000458, -0.000454, -1)
Vector: 0.026, 73.31, 61.531)

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Components

#1: Protein MONO-ADP-RIBOSYLTRANSFERASE C3 / C3BOT1 / EXOENZYME C3


Mass: 23591.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Strain: 468C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P15879, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-V4O / CYCLO-TETRAMETAVANADATE


Mass: 395.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O12V4
#3: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: VO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.5
Details: 18% PEG3350, 3% SAT. NA3VO4, 0.15M NACL,0.1M IMIDAZOLE/MALATE, PH5.5, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 29, 2002 / Details: RH-COATED SI MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 41904 / % possible obs: 91.6 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 15.3
Reflection shellResolution: 1.89→1.96 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4.4 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G24

1g24


Resolution: 1.89→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.144 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2121 5.1 %RANDOM
Rwork0.205 ---
obs0.207 39752 91.5 %-
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: 30.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---1.28 Å20 Å2
3---2.55 Å2
Refinement stepCycle: LAST / Resolution: 1.89→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 0 43 308 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223407
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.6441.974584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr6.2595420
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022492
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21487
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.58722091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47633357
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6944.51316
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2461227
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: 1.89→1.99 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.277 348
Rwork0.208 5837

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