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- PDB-7ce2: The Crystal structure of TeNT Hc complexed with neutralizing antibody -

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Basic information

Entry
Database: PDB / ID: 7ce2
TitleThe Crystal structure of TeNT Hc complexed with neutralizing antibody
Components
  • Tetanus toxin
  • neutralizing antibody heavy chain
  • neutralizing antibody light chain
KeywordsHYDROLASE / antibody
Function / homology
Function and homology information


metallopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium tetani (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsWang, X. / Wang, Y. / Wu, C. / Yu, J. / Liao, H.
CitationJournal: Cell Rep / Year: 2021
Title: Structural basis of tetanus toxin neutralization by native human monoclonal antibodies.
Authors: Wang, Y. / Wu, C. / Yu, J. / Lin, S. / Liu, T. / Zan, L. / Li, N. / Hong, P. / Wang, X. / Jia, Z. / Li, J. / Wang, Y. / Zhang, M. / Yuan, X. / Li, C. / Xu, W. / Zheng, W. / Wang, X. / Liao, H.X.
History
DepositionJun 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetanus toxin
Z: neutralizing antibody heavy chain
B: neutralizing antibody light chain


Theoretical massNumber of molelcules
Total (without water)100,1873
Polymers100,1873
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-25 kcal/mol
Surface area38120 Å2
Unit cell
Length a, b, c (Å)59.690, 136.990, 137.370
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 Tetanus toxin / TeNT Hc


Mass: 52838.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetani (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LA13
#2: Antibody neutralizing antibody heavy chain


Mass: 23926.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody neutralizing antibody light chain


Mass: 23421.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.12 %
Crystal growTemperature: 284 K / Method: vapor diffusion, sitting drop
Details: 3% w/v Dextran sulfate (sodium salt), 0.1M BICINE PH 8.5, 15% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.01→38.067 Å / Num. obs: 75830 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 40.44 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.7
Reflection shellResolution: 2.01→2.12 Å / Num. unique obs: 75830 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A8D

1a8d


Resolution: 2.01→38.067 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 3699 4.89 %
Rwork0.1801 72009 -
obs0.1819 75708 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.75 Å2 / Biso mean: 54.7428 Å2 / Biso min: 26.35 Å2
Refinement stepCycle: final / Resolution: 2.01→38.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6885 0 0 293 7178
Biso mean---53.78 -
Num. residues----874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087045
X-RAY DIFFRACTIONf_angle_d0.9699579
X-RAY DIFFRACTIONf_chiral_restr0.061070
X-RAY DIFFRACTIONf_plane_restr0.0051221
X-RAY DIFFRACTIONf_dihedral_angle_d13.274203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.01-2.03650.31641710.2952681
2.0365-2.06440.29381630.26942742
2.0644-2.09390.30711400.25732711
2.0939-2.12510.28531580.24892719
2.1251-2.15830.2691340.22982731
2.1583-2.19370.2541180.22042766
2.1937-2.23150.24141580.21762722
2.2315-2.27210.24431130.21132744
2.2721-2.31580.25481460.19582740
2.3158-2.3630.19741530.19662743
2.363-2.41440.24091440.19352754
2.4144-2.47060.23661220.20152746
2.4706-2.53230.24891300.1952785
2.5323-2.60080.2731330.20472753
2.6008-2.67730.22921480.19462749
2.6773-2.76370.24031270.19792760
2.7637-2.86250.2541530.19852771
2.8625-2.9770.22831660.20322740
2.977-3.11240.21131400.19652764
3.1124-3.27650.27391590.19572748
3.2765-3.48160.23621390.18962808
3.4816-3.75020.22191580.16862782
3.7502-4.12720.19381000.16132850
4.1272-4.72350.1591630.1372804
4.7235-5.94740.18271320.14882884
5.9474-38.0670.18991310.16943012
Refinement TLS params.Method: refined / Origin x: 61.2251 Å / Origin y: 155.357 Å / Origin z: 286.6931 Å
111213212223313233
T0.2183 Å2-0.0064 Å2-0.0138 Å2-0.2992 Å20.0129 Å2--0.3117 Å2
L0.2189 °20.0435 °2-0.0947 °2-1.1637 °20.6072 °2--0.8274 °2
S-0.0311 Å °-0.0513 Å °-0.0238 Å °-0.0758 Å °0.089 Å °-0.1343 Å °-0.0715 Å °0.08 Å °-0.0551 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA869 - 1315
2X-RAY DIFFRACTION1allZ1 - 221
3X-RAY DIFFRACTION1allB1 - 212
4X-RAY DIFFRACTION1allS1 - 293

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