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- PDB-8h3y: Bacteroide Fragilis Toxin in complex with nanobody 327 -

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Basic information

Entry
Database: PDB / ID: 8h3y
TitleBacteroide Fragilis Toxin in complex with nanobody 327
Components
  • Fragilysin
  • Nanobody 327
KeywordsTOXIN / Bacteroide Fragilis Toxin / nanobody
Function / homology
Function and homology information


fragilysin / metallopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Fragilysin / Fragilysin, N-terminal / Fragilysin, N-terminal domain superfamily / N-terminal domain of fragilysin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Biological speciesBacteroides fragilis (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWen, Y. / Guo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Front Immunol / Year: 2023
Title: Screening and epitope characterization of diagnostic nanobody against total and activated Bacteroides fragilis toxin.
Authors: Guo, Y. / Ouyang, Z. / He, W. / Zhang, J. / Qin, Q. / Jiao, M. / Muyldermans, S. / Zheng, F. / Wen, Y.
History
DepositionOct 9, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fragilysin
B: Fragilysin
D: Nanobody 327
E: Nanobody 327
F: Nanobody 327
C: Fragilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,8789
Polymers175,6816
Non-polymers1963
Water10,953608
1
A: Fragilysin
F: Nanobody 327
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6263
Polymers58,5602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fragilysin
D: Nanobody 327
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6263
Polymers58,5602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Nanobody 327
C: Fragilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6263
Polymers58,5602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.901, 82.984, 139.807
Angle α, β, γ (deg.)90.00, 109.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-592-

HOH

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Components

#1: Protein Fragilysin / Enterotoxin


Mass: 44449.906 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: btfP / Production host: Escherichia coli (E. coli) / References: UniProt: P54355, fragilysin
#2: Antibody Nanobody 327


Mass: 14110.546 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 608 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350, pH 6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→41.39 Å / Num. obs: 152840 / % possible obs: 98.52 % / Redundancy: 3.4 % / Biso Wilson estimate: 41.43 Å2 / CC1/2: 0.984 / Net I/σ(I): 8.4
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 7917 / CC1/2: 0.541

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P24

3p24


Resolution: 2.25→41.39 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0.56 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 3843 2.51 %
Rwork0.2039 --
obs0.2049 152840 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11048 0 3 608 11659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811340
X-RAY DIFFRACTIONf_angle_d0.96515375
X-RAY DIFFRACTIONf_dihedral_angle_d6.4911556
X-RAY DIFFRACTIONf_chiral_restr0.0551670
X-RAY DIFFRACTIONf_plane_restr0.0071995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.270.37081330.34424993X-RAY DIFFRACTION87
2.27-2.30.36571320.34085348X-RAY DIFFRACTION92
2.3-2.340.34621500.33145615X-RAY DIFFRACTION97
2.34-2.370.37521410.32975534X-RAY DIFFRACTION97
2.37-2.40.36631430.31575549X-RAY DIFFRACTION97
2.4-2.440.33711410.30825574X-RAY DIFFRACTION97
2.44-2.480.34991410.29845533X-RAY DIFFRACTION97
2.48-2.520.29631470.29285627X-RAY DIFFRACTION97
2.52-2.570.33971450.2865475X-RAY DIFFRACTION97
2.57-2.620.33531410.28095573X-RAY DIFFRACTION96
2.62-2.670.30611430.28055584X-RAY DIFFRACTION96
2.67-2.730.33831380.27735395X-RAY DIFFRACTION95
2.73-2.790.35161360.2665371X-RAY DIFFRACTION92
2.79-2.860.29141420.24515527X-RAY DIFFRACTION97
2.86-2.940.27951410.24535635X-RAY DIFFRACTION98
2.94-3.030.31081430.24165617X-RAY DIFFRACTION98
3.03-3.130.28181460.23415624X-RAY DIFFRACTION98
3.13-3.240.29781480.23225608X-RAY DIFFRACTION97
3.24-3.370.24981450.2125589X-RAY DIFFRACTION97
3.37-3.520.28831460.18985576X-RAY DIFFRACTION97
3.52-3.710.24831350.18745371X-RAY DIFFRACTION93
3.71-3.940.19071490.17625639X-RAY DIFFRACTION98
3.94-4.240.1881450.14965601X-RAY DIFFRACTION97
4.24-4.670.17491460.12725580X-RAY DIFFRACTION97
4.67-5.340.17371390.13285382X-RAY DIFFRACTION94
5.34-6.730.18061450.14835607X-RAY DIFFRACTION97
6.73-41.390.12361420.1445470X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -41.4861 Å / Origin y: -17.138 Å / Origin z: 50.8314 Å
111213212223313233
T0.3446 Å2-0.0014 Å20.0016 Å2-0.3145 Å20.0031 Å2--0.3449 Å2
L0.0528 °20.0035 °20.0285 °2--0.0348 °20.0021 °2--0.1535 °2
S0.021 Å °0.0102 Å °-0.0086 Å °0.0138 Å °0.0029 Å °-0.0232 Å °-0.0139 Å °-0.0127 Å °0 Å °
Refinement TLS groupSelection details: all

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