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- PDB-6zec: Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma ... -

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Basic information

Entry
Database: PDB / ID: 6zec
TitleCrystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody
Components(Fab fragment ...) x 2
KeywordsIMMUNE SYSTEM / Antibody / Fab / Glycosylated / Glycans / lymphoma
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAllen, J.D. / Watanabe, Y. / Crispin, M. / Bowden, T.A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Bloodwise18009 United Kingdom
Cancer Research UKC42023/A29370 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L009528/1 and MR/S007555/1 United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
CitationJournal: Blood / Year: 2021
Title: Insertion of atypical glycans into the tumor antigen-binding site identifies DLBCLs with distinct origin and behavior.
Authors: Chiodin, G. / Allen, J.D. / Bryant, D.J. / Rock, P. / Martino, E.A. / Valle-Argos, B. / Duriez, P.J. / Watanabe, Y. / Henderson, I. / Blachly, J.S. / McCann, K.J. / Strefford, J.C. / ...Authors: Chiodin, G. / Allen, J.D. / Bryant, D.J. / Rock, P. / Martino, E.A. / Valle-Argos, B. / Duriez, P.J. / Watanabe, Y. / Henderson, I. / Blachly, J.S. / McCann, K.J. / Strefford, J.C. / Packham, G. / Geijtenbeek, T.B.H. / Figdor, C.G. / Wright, G.W. / Staudt, L.M. / Burack, R. / Bowden, T.A. / Crispin, M. / Stevenson, F.K. / Forconi, F.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: 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 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab fragment light chain
H: Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6877
Polymers50,0302
Non-polymers6575
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-29 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.330, 60.790, 84.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-622-

HOH

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab fragment light chain


Mass: 24417.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Organ (production host): Embryonic Kidney / Production host: Homo sapiens (human)
#2: Antibody Fab fragment heavy chain


Mass: 25612.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 437 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 25 %w/v Polyethylene Glycol 3350 0.200 M Magnesium Chloride 0.100 M bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→50.61 Å / Num. obs: 57128 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.8
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4169 / CC1/2: 0.49 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NIV

5niv


Resolution: 1.65→50.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.885 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20605 2765 4.8 %RANDOM
Rwork0.1747 ---
obs0.17622 54318 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 42 433 3861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173192
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6545017
X-RAY DIFFRACTIONr_angle_other_deg1.3461.5797487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.2255.318487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43423.548155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5681512
X-RAY DIFFRACTIONr_chiral_restr0.0650.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024711
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02741
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_it1.0992.1741843
X-RAY DIFFRACTIONr_mcbond_other1.0962.1721842
X-RAY DIFFRACTIONr_mcangle_it1.8153.2522328
X-RAY DIFFRACTIONr_mcangle_other1.8153.2542329
X-RAY DIFFRACTIONr_scbond_it1.4622.321813
X-RAY DIFFRACTIONr_scbond_other1.4622.3211814
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3583.4032687
X-RAY DIFFRACTIONr_long_range_B_refined4.9126.264034
X-RAY DIFFRACTIONr_long_range_B_other4.62525.523936
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 230 -
Rwork0.308 3933 -
obs--99.98 %
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)
10.1130.0224-0.12720.1968-0.22960.6888-0.01630.0311-0.0055-0.0014-0.04840.020.0071-0.01860.06470.00670.00840.00120.0673-0.010.024162.950111.358456.2546
20.2798-0.08680.15370.1342-0.18990.3154-0.01910.04070.04390.0309-0.0425-0.0319-0.01050.0440.06160.0378-0.01340.00280.04450.00530.014278.55856.926964.4934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 230
2X-RAY DIFFRACTION2H2 - 224

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