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- PDB-2ec5: Crystal structures reveal a thiol-protease like catalytic triad i... -

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Basic information

Entry
Database: PDB / ID: 2ec5
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 / Cys1159Ser 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
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 9, 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: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Dermonecrotic toxin
B: Dermonecrotic toxin


Theoretical massNumber of molelcules
Total (without water)168,5632
Polymers168,5632
Non-polymers00
Water4,360242
1
A: Dermonecrotic toxin


Theoretical massNumber of molelcules
Total (without water)84,2821
Polymers84,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dermonecrotic toxin


Theoretical massNumber of molelcules
Total (without water)84,2821
Polymers84,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.357, 132.823, 82.546
Angle α, β, γ (deg.)90.00, 114.74, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

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


Mass: 84281.539 Da / Num. of mol.: 2 / Fragment: C-terminal region, residues 569-1285 / Mutation: C1159S
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG 6000, 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: Jul 3, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 59945 / Num. obs: 57847 / % possible obs: 97.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.473 / % possible all: 88.5

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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: 2.6→44.81 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 27.168 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.719 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28632 2921 5.1 %RANDOM
Rwork0.23217 ---
obs0.23491 54694 97.01 %-
all-57615 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.394 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11286 0 0 242 11528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.96615622
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76851420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79924.669544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.812152016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2281564
X-RAY DIFFRACTIONr_chiral_restr0.0810.21708
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028786
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.25965
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.27998
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2486
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4131.57268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.739211442
X-RAY DIFFRACTIONr_scbond_it0.78334825
X-RAY DIFFRACTIONr_scangle_it1.274.54180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 196 -
Rwork0.323 3575 -
obs--87.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1666-0.4513-0.29931.6995-0.481.28750.20490.3763-0.0892-0.4855-0.20530.22520.2681-0.23670.0004-0.08260.1481-0.1272-0.1313-0.0383-0.31287.92996.608543.0047
20.9494-0.7264-0.18091.78660.1171.40810.17870.080.3198-0.1636-0.1673-0.5816-0.04090.4501-0.0115-0.20920.07370.1045-0.0210.13920.066460.83530.367321.9334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA575 - 128536 - 746
2X-RAY DIFFRACTION2BB575 - 128536 - 746

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