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- PDB-6fe4: Crystal structure of the complex between Shiga toxin Stx2 B subun... -

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Basic information

Entry
Database: PDB / ID: 6fe4
TitleCrystal structure of the complex between Shiga toxin Stx2 B subunit and neutralising Nb113
Components
  • Nb113
  • Shiga-like toxin 2 subunit BShiga toxin
KeywordsTOXIN / Complex / Nanobody / Shiga
Function / homology
Function and homology information


modulation of host virulence by virus / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Shiga-like toxin 2 subunit B
Similarity search - Component
Biological speciesEnterobacteria phage 933W (virus)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBernedo, R. / Muyldermans, S. / Sterckx, Y.G.J.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)Research Internship Abroad (BEPE) awarded to Robert Bernedo Brazil
CitationJournal: Toxins (Basel) / Year: 2018
Title: Structural Basis for the Specific Neutralization of Stx2a with a Camelid Single Domain Antibody Fragment.
Authors: Bernedo-Navarro, R.A. / Romao, E. / Yano, T. / Pinto, J. / De Greve, H. / Sterckx, Y.G. / Muyldermans, S.
History
DepositionDec 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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: Shiga-like toxin 2 subunit B
B: Shiga-like toxin 2 subunit B
C: Shiga-like toxin 2 subunit B
D: Shiga-like toxin 2 subunit B
E: Shiga-like toxin 2 subunit B
F: Nb113
G: Nb113
H: Nb113
I: Nb113
J: Nb113


Theoretical massNumber of molelcules
Total (without water)104,47510
Polymers104,47510
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16260 Å2
ΔGint-46 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.490, 186.490, 75.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Shiga-like toxin 2 subunit B / Shiga toxin / SLT-IIb / Verocytotoxin 2 subunit B / Verotoxin 2 subunit B


Mass: 8066.861 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage 933W (virus) / Gene: stxB2, stx2B, L0104 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P09386
#2: Antibody
Nb113


Mass: 12828.161 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4000, 100 mM sodium citrate pH 5.6, 200 mM ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3→47.47 Å / Num. obs: 30120 / % possible obs: 99.5 % / Redundancy: 7.442 % / Biso Wilson estimate: 122.18 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.168 / Χ2: 0.999 / Net I/σ(I): 9.31 / Num. measured all: 224157 / Scaling rejects: 69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.082.8782.1410.525975219220760.1222.61394.7
3.08-3.162.9081.5350.726322220121740.1881.87998.8
3.16-3.255.8941.6191.212325209520910.4231.76399.8
3.25-3.358.5891.278217444203220310.5861.36100
3.35-3.468.4720.9582.7616994200620060.7521.02100
3.46-3.588.3710.6883.9316130192719270.8560.733100
3.58-3.728.3170.5175.0115319184218420.8980.551100
3.72-3.878.2990.4096.1514889179417940.9460.437100
3.87-4.048.3740.2738.6614261170317030.9770.291100
4.04-4.248.3990.19411.1613816164516450.9870.207100
4.24-4.478.710.15813.0913623156415640.9910.168100
4.47-4.748.5610.11616.3912765149114910.9930.124100
4.74-5.078.4830.10617.8911783138913890.9940.113100
5.07-5.488.5580.10218.2611160130413040.9950.108100
5.48-68.4960.10817.3310144119511940.9920.11699.9
6-6.718.4080.09618.769257110111010.9950.102100
6.71-7.748.1890.07821.2479119669660.9970.083100
7.74-9.4880.06125.9165368178170.9970.066100
9.48-13.417.5660.05427.7348806456450.9970.058100
13.41-47.477.2860.0728.6726233693600.9930.07697.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GA4

2ga4


Resolution: 3→47.47 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 1.067 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.835 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.302
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1506 5 %RANDOM
Rwork0.169 ---
obs0.171 30119 99.6 %-
Displacement parametersBiso max: 230.61 Å2 / Biso mean: 119.53 Å2 / Biso min: 59.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.8332 Å20 Å20 Å2
2---0.8332 Å20 Å2
3---1.6664 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 3→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7084 0 0 44 7128
Biso mean---91.03 -
Num. residues----940
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2393SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1071HARMONIC5
X-RAY DIFFRACTIONt_it7240HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion921SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8000SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7240HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9820HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion21.66
LS refinement shellResolution: 3→3.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2757 140 4.98 %
Rwork0.2678 2674 -
all0.2682 2814 -
obs--96.14 %
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)
12.72970.59540.09242.4772-0.67788.58730.1437-0.1934-0.4688-0.0883-0.1258-0.76450.90781.1628-0.0178-0.03410.390.03040.9405-0.04630.5693-12.49159.09613.224
26.4376-0.36151.08915.32611.43364.44310.18191.0182-0.3067-0.507-0.2181-0.69560.33760.79770.03620.02520.17090.26971.0517-0.03290.2376-18.90269.633-3.088
35.0529-0.44410.14368.5253-1.00613.92820.33820.9633-0.3034-0.6731-0.2224-0.13771.00950.6473-0.11580.28920.10740.04820.554-0.2347-0.0272-37.29562.48-7.578
45.9015-3.0459-1.09655.4790.23165.1790.12750.7702-0.7841-0.6118-0.08640.12631.2965-0.0964-0.0410.7497-0.0349-0.18540.322-0.28920.5677-41.76647.4695.049
59.0708-0.6324-1.55013.7433-2.74923.16560.0231-0.2503-1.0542-0.08420.0645-0.241.23170.6643-0.08750.71030.2979-0.13110.4951-0.04510.8075-26.30645.5117.78
64.1574-1.92022.34564.8686-2.01655.44680.29310.5731-0.00520.1374-0.27940.10790.21240.1055-0.0138-0.1929-0.17980.05830.19210.0458-0.1144-50.63380.695-4.492
76.57260.6077-1.7815.0246-0.56567.51850.50590.47211.071-0.3921-0.2599-0.8233-1.30430.9615-0.2460.2292-0.36380.21880.78860.18270.4798-19.47690.3545.472
87.5358-1.04840.10232.3316-0.24394.5420.0412-0.6938-0.11940.4215-0.1883-0.49440.05761.12470.147-0.0653-0.0491-0.20220.96560.06440.3213-12.69471.76833.045
96.16830.757-1.18227.685-3.84975.87330.2626-1.5124-0.99740.763-0.08860.02850.78180.7886-0.1740.589-0.0677-0.13880.88520.30680.6179-36.34249.85937.413
107.98860.16534.72756.52970.327214.2270.0288-0.3425-0.14930.1168-0.19250.71570.1627-1.60230.16370.0741-0.2211-0.10250.2529-0.09980.3633-60.98855.339914.482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|21 - A|89 }A21 - 89
2X-RAY DIFFRACTION2{ E|20 - E|90 }E20 - 90
3X-RAY DIFFRACTION3{ D|20 - D|89 }D20 - 89
4X-RAY DIFFRACTION4{ C|20 - C|89 }C20 - 89
5X-RAY DIFFRACTION5{ B|20 - B|89 }B20 - 89
6X-RAY DIFFRACTION6{ I|1 - I|118 }I1 - 118
7X-RAY DIFFRACTION7{ J|1 - J|116 }J1 - 116
8X-RAY DIFFRACTION8{ F|1 - F|116 }F1 - 116
9X-RAY DIFFRACTION9{ G|1 - G|116 }G1 - 116
10X-RAY DIFFRACTION10{ H|1 - H|117 }H1 - 117

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