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- PDB-8tn4: The Crystal Structure of a human monoclonal antibody (aAb), terme... -

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Basic information

Entry
Database: PDB / ID: 8tn4
TitleThe Crystal Structure of a human monoclonal antibody (aAb), termed TG10, used to study poly-N-acetyl-glucosamine broadly expressed in biofilm-forming pathogenclonal antibody
Components
  • TG10, Heavy chain
  • TG10, Light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / TG10 / PANG
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLi, M. / Wlodawer, A. / Temme, S. / Gildersleeve, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cell Chem Biol / Year: 2024
Title: Insights into biofilm architecture and maturation enable improved clinical strategies for exopolysaccharide-targeting therapeutics.
Authors: Temme, J.S. / Tan, Z. / Li, M. / Yang, M. / Wlodawer, A. / Huang, X. / Schneekloth Jr., J.S. / Gildersleeve, J.C.
History
DepositionAug 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: TG10, Heavy chain
L: TG10, Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,73920
Polymers47,0832
Non-polymers1,65618
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-232 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.254, 90.254, 208.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11H-305-

SO4

21H-636-

HOH

31L-621-

HOH

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Components

#1: Antibody TG10, Heavy chain


Mass: 23403.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody TG10, Light chain


Mass: 23680.141 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 2.4 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 96536 / % possible obs: 97.2 % / Redundancy: 18 % / CC star: 1 / Rmerge(I) obs: 0.73 / Net I/σ(I): 40.25
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.884 / Num. unique obs: 3362 / CC star: 0.751

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→45.17 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.791 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16999 2750 3.1 %RANDOM
Rwork0.13546 ---
obs0.13652 86851 90.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.233 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0.29 Å20 Å2
2---0.59 Å20 Å2
3---1.91 Å2
Refinement stepCycle: 1 / Resolution: 1.4→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 86 603 3999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123541
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163166
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.6414845
X-RAY DIFFRACTIONr_angle_other_deg0.5781.5647369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3765448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.633516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53710566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02775
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1451.5961759
X-RAY DIFFRACTIONr_mcbond_other2.1271.5961759
X-RAY DIFFRACTIONr_mcangle_it2.9362.8772200
X-RAY DIFFRACTIONr_mcangle_other2.9462.8782201
X-RAY DIFFRACTIONr_scbond_it2.111.8421782
X-RAY DIFFRACTIONr_scbond_other1.9481.7981715
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6333.162538
X-RAY DIFFRACTIONr_long_range_B_refined5.16122.664040
X-RAY DIFFRACTIONr_long_range_B_other4.3818.743790
X-RAY DIFFRACTIONr_rigid_bond_restr5.01536707
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.739 57 -
Rwork0.783 2173 -
obs--30.93 %

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