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- PDB-8tn5: The Crystal Structure of a human monoclonal antibody (aAb), terme... -

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Basic information

Entry
Database: PDB / ID: 8tn5
TitleThe Crystal Structure of a human monoclonal antibody (aAb), termed TG10, complexed with a GlcNH2
Components
  • TG10, Heavy chain
  • TG10, Light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / TG10 / GlcNac
Function / homology2-amino-2-deoxy-beta-D-glucopyranose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 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)48,06612
Polymers47,0832
Non-polymers98310
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-106 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.524, 90.524, 207.300
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-303-

SO4

21H-567-

HOH

31L-555-

HOH

41L-601-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#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)

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 432 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.4M 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 EIGER X 16M / Detector: PIXEL / Date: Sep 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→78.4 Å / Num. obs: 49758 / % possible obs: 98.2 % / Redundancy: 18.3 % / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 28.1
Reflection shellResolution: 1.76→1.8 Å / Rmerge(I) obs: 0.632 / Num. unique obs: 9073 / CC1/2: 0.749

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→78.4 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.184 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20622 1025 2.1 %RANDOM
Rwork0.16393 ---
obs0.16482 48642 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.763 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å2-0 Å2
2--0.05 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.76→78.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 53 423 3786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123478
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163153
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.6454745
X-RAY DIFFRACTIONr_angle_other_deg0.5771.5667323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4825448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.471516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2710555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02774
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_it1.9691.791759
X-RAY DIFFRACTIONr_mcbond_other1.9641.791759
X-RAY DIFFRACTIONr_mcangle_it2.8843.1982200
X-RAY DIFFRACTIONr_mcangle_other2.8833.2012201
X-RAY DIFFRACTIONr_scbond_it3.1132.0971719
X-RAY DIFFRACTIONr_scbond_other3.1122.0991720
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5893.6922540
X-RAY DIFFRACTIONr_long_range_B_refined7.98324.433912
X-RAY DIFFRACTIONr_long_range_B_other7.98224.443913
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.761→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 60 -
Rwork0.239 2910 -
obs--80.77 %
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)
10.3856-0.11160.32720.2731-0.27430.4214-0.0167-0.0139-0.0305-0.00840.0107-0.0126-0.0291-0.02420.00610.08420.0088-0.01130.064-0.00960.063118.027719.8775101.7358
21.158-0.00751.26870.7422-0.01151.3915-0.1928-0.22650.2022-0.1216-0.03050.0046-0.2032-0.24820.22330.09480.0312-0.0670.0614-0.03840.123525.182854.2911111.1566
30.2769-0.29080.12510.3404-0.05350.2609-0.01150.02240.0250.0365-0.0189-0.02920.0174-0.01420.03040.07350.0144-0.0090.0683-0.01250.07356.362429.16985.8361
46.52960.21592.16190.5880.82361.6918-0.30860.14430.3118-0.24020.07980.0924-0.40570.14870.22870.1169-0.0511-0.08470.03410.06980.153517.554757.451593.4799
53.86731.79891.05980.9070.53750.3189-0.1422-0.00480.0357-0.07940.06750.1145-0.04620.03990.07470.0637-0.0037-0.00410.10350.07330.162138.229657.4318106.0749
63.27271.51182.6560.88481.43922.4052-0.37320.4042-0.3032-0.28680.40290.0218-0.44630.5378-0.02970.1132-0.1468-0.06550.27720.11330.185925.807852.812394.1777
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 127
2X-RAY DIFFRACTION2L128 - 234
3X-RAY DIFFRACTION3H1 - 128
4X-RAY DIFFRACTION4H129 - 140
5X-RAY DIFFRACTION5H141 - 150
6X-RAY DIFFRACTION6H151 - 231

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