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- PDB-6zz5: Structure of soluble SmhB of the tripartite alpha-pore forming to... -

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Basic information

Entry
Database: PDB / ID: 6zz5
TitleStructure of soluble SmhB of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.
ComponentsSmhB
KeywordsTOXIN / Pore forming toxin / Bacterial toxin / Serratia marcescens
Function / homologyHemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / membrane / HBL/NHE enterotoxin family protein
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsChurchill-Angus, A.M. / Baker, P.J.
CitationJournal: Sci Rep / Year: 2021
Title: Characterisation of a tripartite alpha-pore forming toxin from Serratia marcescens
Authors: Churchill-Angus, A.M. / Schofield, T.H.B. / Marlow, T.R. / Sedelnikova, S.E. / Wilson, J.S. / Rafferty, J.B. / Baker, P.J.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: SmhB
BBB: SmhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,95617
Polymers78,7532
Non-polymers1,20315
Water4,630257
1
AAA: SmhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,10510
Polymers39,3771
Non-polymers7299
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: SmhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8517
Polymers39,3771
Non-polymers4746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.940, 113.950, 130.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein SmhB / SmhB


Mass: 39376.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SmhB / Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: BHU62_20105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Q4NVM7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 280.15 K / Method: vapor diffusion, sitting drop / Details: 0.17 M ammonium sulphate, 25.5 % PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.84→65.185 Å / Num. obs: 66582 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.078 / Net I/σ(I): 9.5
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 1.214 / Mean I/σ(I) obs: 1 / Num. unique obs: 3207 / CC1/2: 0.5 / Rpim(I) all: 0.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GRK

6grk


Resolution: 1.84→65.185 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.18 / SU B: 7.039 / SU ML: 0.1 / Average fsc free: 0.9075 / Average fsc work: 0.9137 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.224 3268 4.914 %
Rwork0.1872 63238 -
all0.189 --
obs-66506 99.661 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.839 Å2
Baniso -1Baniso -2Baniso -3
1--0.509 Å20 Å2-0 Å2
2---1.266 Å20 Å2
3---1.775 Å2
Refinement stepCycle: LAST / Resolution: 1.84→65.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5389 0 68 257 5714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135598
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175273
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.6277609
X-RAY DIFFRACTIONr_angle_other_deg1.5421.5712240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9725752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93923.62279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55515976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1561534
X-RAY DIFFRACTIONr_chiral_restr0.0980.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021057
X-RAY DIFFRACTIONr_nbd_refined0.2170.21298
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.24726
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22904
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3910.232
X-RAY DIFFRACTIONr_nbd_other0.1920.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3290.221
X-RAY DIFFRACTIONr_mcbond_it3.131.4052903
X-RAY DIFFRACTIONr_mcbond_other3.1151.4052902
X-RAY DIFFRACTIONr_mcangle_it3.5922.0823633
X-RAY DIFFRACTIONr_mcangle_other3.5962.0833634
X-RAY DIFFRACTIONr_scbond_it6.341.9812695
X-RAY DIFFRACTIONr_scbond_other6.341.9822696
X-RAY DIFFRACTIONr_scangle_it8.0012.733957
X-RAY DIFFRACTIONr_scangle_other82.7313958
X-RAY DIFFRACTIONr_lrange_it8.51318.4626517
X-RAY DIFFRACTIONr_lrange_other8.51218.4696518
X-RAY DIFFRACTIONr_ncsr_local_group_10.1420.0510892
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.84-1.8880.3342300.30545620.30748990.7280.73397.81590.309
1.888-1.9390.3292110.28344600.28547030.7840.79999.31960.285
1.939-1.9960.2892200.25743620.25845920.8420.84699.78220.255
1.996-2.0570.2662040.22842640.2344920.8920.88999.46570.221
2.057-2.1240.2212130.20841690.20843990.9170.91999.61350.196
2.124-2.1990.222310.18639540.18741900.9320.93799.88070.172
2.199-2.2820.2082100.16138560.16340700.9410.95499.90170.145
2.282-2.3750.2121920.16737390.1739350.9370.95199.89840.151
2.375-2.480.21880.15835750.1637670.9460.95699.89380.143
2.48-2.6010.2371730.16534230.16835980.9350.9599.94440.15
2.601-2.7420.1981830.16432570.16634400.9520.9561000.147
2.742-2.9080.2121790.16531160.16732950.9470.9571000.15
2.908-3.1080.2051530.16829170.1730700.9530.9551000.158
3.108-3.3560.2161450.18727350.18828820.940.95399.93060.177
3.356-3.6760.2561260.1925340.19326620.9340.95599.92490.185
3.676-4.1080.2061160.17822940.17924100.9550.9631000.177
4.108-4.740.172990.1520450.15121470.9660.97299.86030.154
4.74-5.7980.228860.19717500.19918380.9550.96399.89120.203
5.798-8.1670.249700.19713950.214650.9630.9721000.203
8.167-65.1850.199390.228310.2198770.9840.97999.20180.275
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)
10.4275-0.13430.01021.97890.17450.34180.01070.01130.04510.0614-0.02520.0292-0.0419-0.02170.01440.08320.0050.00160.0576-0.00990.0078-3.179316.8029-11.9582
20.5750.5469-0.16851.2631-0.29980.2876-0.00310.01620.0033-0.0197-0.0126-0.07880.00980.0530.01570.10970.01770.00170.0641-0.00330.043217.424211.3975-39.823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 360
2X-RAY DIFFRACTION2ALLBBB2 - 364

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