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- PDB-6rim: Crystal structure of the catalytic domain of the Weissela oryzae ... -

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Basic information

Entry
Database: PDB / ID: 6rim
TitleCrystal structure of the catalytic domain of the Weissela oryzae botulinum like toxin
ComponentsPutative botulinum-like toxin Wo
KeywordsTOXIN / botulinum neurotoxin / zinc endopeptidase
Function / homologybontoxilysin / Kunitz inhibitor STI-like superfamily / metalloendopeptidase activity / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / proteolysis / metal ion binding / Putative botulinum-like toxin Wo
Function and homology information
Biological speciesWeissella oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKosenina, S. / Masuyer, G. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03406 Sweden
CitationJournal: Febs Lett. / Year: 2019
Title: Crystal structure of the catalytic domain of the Weissella oryzae botulinum-like toxin.
Authors: Kosenina, S. / Masuyer, G. / Zhang, S. / Dong, M. / Stenmark, P.
History
DepositionApr 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative botulinum-like toxin Wo
B: Putative botulinum-like toxin Wo
C: Putative botulinum-like toxin Wo
D: Putative botulinum-like toxin Wo
E: Putative botulinum-like toxin Wo
F: Putative botulinum-like toxin Wo
G: Putative botulinum-like toxin Wo
H: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,21024
Polymers458,3668
Non-polymers84416
Water61,4853413
1
A: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Putative botulinum-like toxin Wo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4013
Polymers57,2961
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.908, 105.208, 179.621
Angle α, β, γ (deg.)101.71, 90.00, 90.00
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative botulinum-like toxin Wo / BoNT/Wo


Mass: 57295.812 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella oryzae (bacteria) / Gene: WOSG25_110680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A069CUU9, bontoxilysin
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3413 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 0.2 M CaCl2 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→58.63 Å / Num. obs: 531729 / % possible obs: 97.1 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.06 / Rrim(I) all: 0.11 / Net I/σ(I): 6.74
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.6 % / Num. unique obs: 25808 / CC1/2: 0.472 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→58.63 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.899 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20169 26608 5 %RANDOM
Rwork0.15074 ---
obs0.15328 505114 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.266 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å2-0.75 Å21.41 Å2
2---0.22 Å2-1.66 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.6→58.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29021 0 16 3415 32452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01329976
X-RAY DIFFRACTIONr_bond_other_d0.0120.01726444
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.64840609
X-RAY DIFFRACTIONr_angle_other_deg1.4611.57761595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32853633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56323.1311750
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.443154869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.38615165
X-RAY DIFFRACTIONr_chiral_restr0.0660.23873
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0234029
X-RAY DIFFRACTIONr_gen_planes_other0.0030.026686
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8592.78114490
X-RAY DIFFRACTIONr_mcbond_other2.85914489
X-RAY DIFFRACTIONr_mcangle_it3.72818137
X-RAY DIFFRACTIONr_mcangle_other3.72818138
X-RAY DIFFRACTIONr_scbond_it3.81815486
X-RAY DIFFRACTIONr_scbond_other3.81415484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.67722472
X-RAY DIFFRACTIONr_long_range_B_refined6.0534322
X-RAY DIFFRACTIONr_long_range_B_other5.67533396
X-RAY DIFFRACTIONr_rigid_bond_restr10.856329889
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 1868 -
Rwork0.281 36829 -
obs--95.24 %

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