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- PDB-7nmq: Bacillus cereus HblL1 toxin component -

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Basic information

Entry
Database: PDB / ID: 7nmq
TitleBacillus cereus HblL1 toxin component
ComponentsHemolysin BL lytic component L1
KeywordsTOXIN / Bacillus cereus / Haemolysin BL / alpha helical pore forming toxin
Function / homology
Function and homology information


Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Hemolysin BL lytic component L1
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsRizkallah, P.J. / Berry, C.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Toxins / Year: 2021
Title: The Crystal Structure of Bacillus cereus HblL 1 .
Authors: Worthy, H.L. / Williamson, L.J. / Auhim, H.S. / Leppla, S.H. / Sastalla, I. / Jones, D.D. / Rizkallah, P.J. / Berry, C.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 21, 2021Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.3Apr 28, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Hemolysin BL lytic component L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9748
Polymers39,4071
Non-polymers5677
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint17 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.660, 72.960, 133.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemolysin BL lytic component L1 / Hemolysin BL-binding component / Hemolysin D / Hemolytic enterotoxin HBL lytic component L1


Mass: 39407.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: hblD, hblA_3, hblA_5, A9485_22250, B4080_2259, BACERE00184_05564, BLD50_23415, BLX06_15130, C1N66_23990, C6A78_05365, C6Y54_18295, CJ306_16805, CN357_02795, CN490_15095, CN508_00570, CN516_ ...Gene: hblD, hblA_3, hblA_5, A9485_22250, B4080_2259, BACERE00184_05564, BLD50_23415, BLX06_15130, C1N66_23990, C6A78_05365, C6Y54_18295, CJ306_16805, CN357_02795, CN490_15095, CN508_00570, CN516_18660, CN950_19490, CN959_26890, CN980_29445, COA01_24215, COA24_28650, COA26_17090, COC69_20455, COD14_28250, COD86_04255, COI98_28045, COK33_32670, CON36_29700, CON37_30715, CSW12_15440, D0437_29230, DR116_0005010, FC693_25985, FHP23_10995, FHR06_03165, FOC92_03975, FORC47_2296, FXB61_000321, HLB41_12235, NCTC7464_00229, TU58_21945, TU68_26310
Production host: Bacillus anthracis (anthrax bacterium) / Strain (production host): BH460 / References: UniProt: Q1XBV1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M cacodylate Bis Tris propionate, 25% w/v PEG 1500, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.36→64.05 Å / Num. obs: 77106 / % possible obs: 99.3 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.384.61.3571687636980.3970.7011.534199
7.45-63.975.10.02228735650.9990.0110.0253698.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KUD

5kud


Resolution: 1.36→64.05 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.516 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0632 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 3764 4.9 %RANDOM
Rwork0.1623 ---
obs0.1641 73264 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.75 Å2 / Biso mean: 17.393 Å2 / Biso min: 10.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--1.12 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 1.36→64.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 37 489 3295
Biso mean--32.58 29.81 -
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172962
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.634164
X-RAY DIFFRACTIONr_angle_other_deg1.6211.5876859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3655415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93526.741135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20315556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.889154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023647
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02649
X-RAY DIFFRACTIONr_rigid_bond_restr5.6733035
LS refinement shellResolution: 1.36→1.395 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 281 -
Rwork0.332 5260 -
all-5541 -
obs--98.77 %
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)
10.35760.83920.20332.64160.64050.1951-0.0041-0.0035-0.00530.03240.01190.01090.0198-0.0054-0.00770.0754-0.0043-0.00170.00260.00050.121716.92593.57111.824
21.33160.9084-0.021.205-0.18360.87550.0054-0.01880.044-0.040.0120.0186-0.0451-0.0015-0.01740.04980.00420.00170.00560.0060.1358.644108.39826.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 210
2X-RAY DIFFRACTION1A315 - 406
3X-RAY DIFFRACTION2A211 - 314

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