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- PDB-2c89: Structure of the wild-type C3bot1 Exoenzyme (Free state, crystal ... -

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Basic information

Entry
Database: PDB / ID: 2c89
TitleStructure of the wild-type C3bot1 Exoenzyme (Free state, crystal form I)
ComponentsMONO-ADP-RIBOSYLTRANSFERASE C3
KeywordsTRANSFERASE / C3 EXOENZYME / ARTT MOTIF / BACTERIAL TOXINS / GLYCOSYLTRANSFERASE
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 / Exoenzyme C3
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStura, E.A. / Menetrey, J. / Flatau, G. / Boquet, P. / Menez, A.
Citation
Journal: Protein Sci. / Year: 2008
Title: Structural Basis for the Nad-Hydrolysis Mechanism and the Artt-Loop Plasticity of C3 Exoenzymes.
Authors: Menetrey, J. / Flatau, G. / Boquet, P. / Menez, A. / Stura, E.A.
#1: Journal: 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. / Ledu, M.H. / Boquet, P. / Menez, A.
History
DepositionDec 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
C: MONO-ADP-RIBOSYLTRANSFERASE C3
D: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6567
Polymers94,3684
Non-polymers2883
Water10,557586
1
A: MONO-ADP-RIBOSYLTRANSFERASE C3


Theoretical massNumber of molelcules
Total (without water)23,5921
Polymers23,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6882
Polymers23,5921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6882
Polymers23,5921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6882
Polymers23,5921
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.456, 74.820, 120.442
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MONO-ADP-RIBOSYLTRANSFERASE C3 / EXOENZYME 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) / Strain (production host): BL21
References: UniProt: P15879, UniProt: Q7M0L1*PLUS, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.38 Å3/Da / Density % sol: 47.89 %
Crystal growDetails: 22.5% PEG 3350 W/W, 100 MM LI2SO4, 100 MM SODIUM CITRATE PH 3.0, 3-10% MPEG 550 V/V

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.85→45.18 Å / Num. obs: 77456 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.8

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Processing

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

1gzf


Resolution: 1.85→45.18 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.179 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3893 5 %RANDOM
Rwork0.208 ---
obs0.21 73562 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: 27.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.79 Å2
2--1.54 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6376 0 15 586 6977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226509
X-RAY DIFFRACTIONr_bond_other_d0.0020.025858
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9618743
X-RAY DIFFRACTIONr_angle_other_deg0.714313772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3775806
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_restr0.0610.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021257
X-RAY DIFFRACTIONr_nbd_refined0.1870.21265
X-RAY DIFFRACTIONr_nbd_other0.2310.26544
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.23572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2405
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4921.54016
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94726455
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41732493
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4354.52288
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 268
Rwork0.251 5396

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