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- PDB-2c8d: Structure of the ARTT motif Q212A mutant C3bot1 Exoenzyme (Free s... -

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Basic information

Entry
Database: PDB / ID: 2c8d
TitleStructure of the ARTT motif Q212A mutant 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: 2.2 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

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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)94,6209
Polymers94,1404
Non-polymers4805
Water3,135174
1
A: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7273
Polymers23,5351
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6312
Polymers23,5351
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6312
Polymers23,5351
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)23,6312
Polymers23,5351
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.399, 74.742, 121.178
Angle α, β, γ (deg.)90.00, 102.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23534.918 Da / Num. of mol.: 4 / Mutation: YES
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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Compound detailsADP-RIBOSYLATES EUKARYOTIC RHO AND RAC PROTEINS ON AN ASPARAGINE RESIDUE ENGINEERED RESIDUE IN ...ADP-RIBOSYLATES EUKARYOTIC RHO AND RAC PROTEINS ON AN ASPARAGINE RESIDUE ENGINEERED RESIDUE IN CHAIN A, GLN 212 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLN 212 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLN 212 TO ALA ENGINEERED RESIDUE IN CHAIN D, GLN 212 TO ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 50.89 %
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: 2.2→45.18 Å / Num. obs: 40473 / % possible obs: 86.4 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9

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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: 2.2→45.17 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 7.246 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2028 5 %RANDOM
Rwork0.212 ---
obs0.215 38442 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: 36.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-0.53 Å2
2--1.26 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6392 0 25 174 6591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226525
X-RAY DIFFRACTIONr_bond_other_d0.0020.025868
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9638766
X-RAY DIFFRACTIONr_angle_other_deg0.748313786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155811
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_restr0.0680.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027150
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021262
X-RAY DIFFRACTIONr_nbd_refined0.1940.21190
X-RAY DIFFRACTIONr_nbd_other0.2280.26334
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.23712
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2172
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5821.54037
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10826478
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.55432488
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6754.52288
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: 2.2→2.32 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.297 227
Rwork0.26 4927

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