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- PDB-1gir: CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CL... -

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Basic information

Entry
Database: PDB / ID: 1gir
TitleCRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADPH
ComponentsIOTA TOXIN COMPONENT IA
KeywordsTOXIN / enzymatic component
Function / homology
Function and homology information


nucleotide binding / extracellular region
Similarity search - Function
Binary exotoxin A, clostridial type / 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
Chem-NDP / Iota toxin component Ia
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsTsuge, H. / Nagahama, M. / Nishimura, H. / Hisatsune, J. / Sakaguchi, Y. / Itogawa, Y. / Katunuma, N. / Sakurai, J.
CitationJournal: J.MOL.BIOL. / Year: 2003
Title: Crystal Structure and Site-directed Mutagenesis of Enzymatic Components from Clostridium perfringens Iota-toxin
Authors: Tsuge, H. / Nagahama, M. / Nishimura, H. / Hisatsune, J. / Sakaguchi, Y. / Itogawa, Y. / Katunuma, N. / Sakurai, J.
History
DepositionMar 12, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: IOTA TOXIN COMPONENT IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3942
Polymers47,6491
Non-polymers7451
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.600, 88.370, 93.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein IOTA TOXIN COMPONENT IA


Mass: 47648.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium perfringens (bacteria) / References: UniProt: Q46220
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 277 K / Details: PEG4000, NADPH, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme1drop
210 mMTris1droppH7.5
318.5 %(w/v)PEG40001reservoir
416 mMNADPH1reservoir
510 mMTris1reservoirpH7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: ADSC QUANTUM / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 26770 / Num. obs: 26770 / % possible obs: 91.2 % / Redundancy: 1.4 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.297 / % possible all: 78.6
Reflection
*PLUS
Highest resolution: 2.1 Å
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 78.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
CNS1refinement
DPSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 2.1→14.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 370484.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2385 9.8 %RANDOM
Rwork0.205 ---
obs-24246 82.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7813 Å2 / ksol: 0.352911 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.32 Å20 Å2
3---2.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→14.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 48 139 3534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.782.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 232 8.6 %
Rwork0.217 2471 -
obs--56.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2nadph.paramnadph.top
X-RAY DIFFRACTION3water_rep.param
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07

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