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- PDB-2ebh: Crystal structures reveal a thiol-protease like catalytic triad i... -

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Basic information

Entry
Database: PDB / ID: 2ebh
TitleCrystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of Pasteurella multocida toxin
ComponentsDermonecrotic toxinCytotoxic necrotising factor family
KeywordsTOXIN / Pasteurella multocida toxin / Cys1165Ser mutant / inactivated mutant
Function / homology
Function and homology information


symbiont-mediated activation of of host transcription / symbiont-mediated killing of host cell / phospholipase activity / phospholipid binding / toxin activity / host cell plasma membrane / extracellular region / membrane / cytoplasm
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #180 / Rossmann fold - #11550 / : / Pasteurella multocida toxin, C3 domain / Secreted effector protein ssei fold / Secreted effector protein ssei. / : / Pasteurella multocida toxin, C2 domain / Domain of unknown function DUF6543 / Family of unknown function (DUF6543) ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #180 / Rossmann fold - #11550 / : / Pasteurella multocida toxin, C3 domain / Secreted effector protein ssei fold / Secreted effector protein ssei. / : / Pasteurella multocida toxin, C2 domain / Domain of unknown function DUF6543 / Family of unknown function (DUF6543) / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Papain-like cysteine peptidase superfamily / Roll / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
trehalose / Dermonecrotic toxin
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKitadokoro, K. / Horiguchi, Y. / Kamitani, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structures reveal a thiol protease-like catalytic triad in the C-terminal region of Pasteurella multocida toxin
Authors: Kitadokoro, K. / Kamitani, S. / Miyazawa, M. / Hanajima-Ozawa, M. / Fukui, A. / Miyake, M. / Horiguchi, Y.
History
DepositionFeb 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Dermonecrotic toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9663
Polymers84,2821
Non-polymers6852
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.755, 150.559, 77.910
Angle α, β, γ (deg.)90.00, 104.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-317-

HOH

DetailsThe molecule exist as a monomer

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Components

#1: Protein Dermonecrotic toxin / Cytotoxic necrotising factor family / DNT / PMT / Mitogenic toxin


Mass: 84281.539 Da / Num. of mol.: 1 / Fragment: C-terminal region, residues 569-1285 / Mutation: C1165S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: G-7 / Gene: toxA / Plasmid: pPROEX-1, pPROEX-1-C-PMT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17452
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.73 Å3/Da / Density % sol: 67.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0M ammonium citrate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 22, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 48566 / Num. obs: 47787 / % possible obs: 99.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.403 / Num. unique all: 4466 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EBF

2ebf


Resolution: 2.4→43.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.886 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.403 / ESU R: 0.28 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2412 5.1 %RANDOM
Rwork0.21287 ---
all0.21471 47671 --
obs0.213 45259 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.807 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5643 0 46 371 6060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225817
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.9757881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30324.669272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.605151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6031532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024393
X-RAY DIFFRACTIONr_nbd_refined0.1850.22827
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2384
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.219
X-RAY DIFFRACTIONr_mcbond_it0.4781.53647
X-RAY DIFFRACTIONr_mcangle_it0.85125721
X-RAY DIFFRACTIONr_scbond_it0.8632459
X-RAY DIFFRACTIONr_scangle_it1.4864.52160
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 162 -
Rwork0.338 3047 -
obs--90.6 %

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