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- PDB-1giq: Crystal Structure of the Enzymatic Componet of Iota-Toxin from Cl... -

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Basic information

Entry
Database: PDB / ID: 1giq
TitleCrystal Structure of the Enzymatic Componet of Iota-Toxin from Clostridium Perfringens with NADH
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Iota toxin component Ia
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Nov 6, 2013Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
B: IOTA TOXIN COMPONENT IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6284
Polymers95,2972
Non-polymers1,3312
Water5,152286
1
A: IOTA TOXIN COMPONENT IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3142
Polymers47,6491
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IOTA TOXIN COMPONENT IA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3142
Polymers47,6491
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.200, 54.440, 103.380
Angle α, β, γ (deg.)99.20, 93.10, 106.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein IOTA TOXIN COMPONENT IA


Mass: 47648.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridium perfringens (bacteria) / References: UniProt: Q46220
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 277 K / Details: PEG4000, NADH, 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/mlprotein1drop
210 mMTris1droppH7.5
318 %PEG40001reservoir
416 mMNADH1reservoir
510 mMTris1reservoirpH7.5

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Data collection

DiffractionMean temperature: 283 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: 1.8→15 Å / Num. all: 87691 / Num. obs: 87691 / % possible obs: 95.9 % / Redundancy: 1.97 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.256 / % possible all: 93.4
Reflection
*PLUS
Highest resolution: 1.8 Å
Reflection shell
*PLUS
% possible obs: 93.4 %

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Processing

Software
NameClassification
MOSFLMdata reduction
CNSrefinement
DPSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GIR:THE ENZYMATIC COMPONENT IOTA-TOXIN WITH NADPH

1gir


Resolution: 1.8→14.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 454280.27 / Data cutoff high rms absF: 462649.14 / 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
Rfree0.25 8178 9.8 %RANDOM
Rwork0.224 ---
obs-83233 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9806 Å2 / ksol: 0.382578 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.38 Å2-0.11 Å2
2--2.08 Å22.12 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6694 0 88 286 7068
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it2.42
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 1051 8.6 %
Rwork0.269 11160 -
obs--80.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2vip2nad.paramvip2nad.top
X-RAY DIFFRACTION3water_rep.param
Refinement
*PLUS
Highest resolution: 1.8 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_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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