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- PDB-8h3x: Bacteroide Fragilis Toxin in complex with nanobody 282 -

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Basic information

Entry
Database: PDB / ID: 8h3x
TitleBacteroide Fragilis Toxin in complex with nanobody 282
Components
  • Fragilysin
  • nanobody 282
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: 1.66 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
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Fragilysin
A: nanobody 282
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7713
Polymers58,7062
Non-polymers651
Water10,142563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.663, 78.212, 118.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fragilysin / / Enterotoxin


Mass: 44449.906 Da / Num. of mol.: 1
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 282


Mass: 14255.790 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium thiocyanate, 20 % w/v PEG 3350

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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: 1.66→35.17 Å / Num. obs: 117825 / % possible obs: 99.48 % / Redundancy: 12.3 % / CC1/2: 1 / Net I/σ(I): 21.83
Reflection shellResolution: 1.66→1.72 Å / Num. unique obs: 5862 / CC1/2: 0.529

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Processing

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

3p24


Resolution: 1.66→35.17 Å / SU ML: 0.2847 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2164 3839 3.26 %
Rwork0.1832 113986 -
obs0.1843 117825 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.55 Å2
Refinement stepCycle: LAST / Resolution: 1.66→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 1 563 4325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733882
X-RAY DIFFRACTIONf_angle_d1.04055268
X-RAY DIFFRACTIONf_chiral_restr0.0617574
X-RAY DIFFRACTIONf_plane_restr0.0091687
X-RAY DIFFRACTIONf_dihedral_angle_d6.1264536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.4891300.56243816X-RAY DIFFRACTION90.86
1.68-1.70.48241400.45934111X-RAY DIFFRACTION96.24
1.7-1.720.41591400.40424209X-RAY DIFFRACTION98.91
1.72-1.750.34721450.3654278X-RAY DIFFRACTION99.57
1.75-1.770.34121410.3164226X-RAY DIFFRACTION99.93
1.77-1.80.3161430.28644221X-RAY DIFFRACTION99.95
1.8-1.830.27181440.25034204X-RAY DIFFRACTION99.95
1.83-1.860.26651410.2374317X-RAY DIFFRACTION99.91
1.86-1.90.26691430.22164206X-RAY DIFFRACTION99.93
1.9-1.930.36211400.30924143X-RAY DIFFRACTION97.92
1.93-1.970.28081410.22564275X-RAY DIFFRACTION99.95
1.97-2.010.28491440.22734241X-RAY DIFFRACTION99.98
2.01-2.060.23931440.21184305X-RAY DIFFRACTION100
2.06-2.110.24041450.18054227X-RAY DIFFRACTION99.98
2.11-2.170.21061430.1814269X-RAY DIFFRACTION100
2.17-2.230.21961440.18644249X-RAY DIFFRACTION99.91
2.23-2.310.26741420.19744230X-RAY DIFFRACTION99.23
2.31-2.390.23481380.18954226X-RAY DIFFRACTION99.98
2.39-2.480.26021440.18844237X-RAY DIFFRACTION99.95
2.48-2.60.23351400.1874264X-RAY DIFFRACTION100
2.6-2.730.2521440.18454241X-RAY DIFFRACTION99.95
2.73-2.90.19361420.18184265X-RAY DIFFRACTION99.93
2.9-3.130.20731470.17544251X-RAY DIFFRACTION100
3.13-3.440.17751450.16344249X-RAY DIFFRACTION100
3.44-3.940.20021420.14044259X-RAY DIFFRACTION99.95
3.94-4.960.15951390.13214227X-RAY DIFFRACTION99.75
4.96-35.170.14681480.15994240X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 6.48483884525 Å / Origin y: 6.78828129858 Å / Origin z: 14.2373858618 Å
111213212223313233
T0.190570925532 Å20.0211097769467 Å2-0.00708523362085 Å2-0.197473544809 Å20.018518560151 Å2--0.18781209862 Å2
L0.785264497983 °20.411245945685 °2-0.0205011088999 °2-0.858346362249 °2-0.0773239792233 °2--0.526274526045 °2
S0.049065927742 Å °-0.0126457341133 Å °0.0112197496366 Å °0.0254408840092 Å °-0.0428235473183 Å °-0.0328323306552 Å °-0.0250386773945 Å °0.035861487121 Å °-0.0122432915521 Å °
Refinement TLS groupSelection details: all

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