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- PDB-7uen: Genetic and structural basis of the human anti-alpha-galactosyl a... -

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Basic information

Entry
Database: PDB / ID: 7uen
TitleGenetic and structural basis of the human anti-alpha-galactosyl antibody response
Components(M86 antibody Fab ...) x 2
KeywordsIMMUNE SYSTEM / alpha-galactosyl / antibody / anti-alpha-gal / immune response / M86
Function / homology: / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsLangley, D.B. / Christ, D.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Genetic and structural basis of the human anti-alpha-galactosyl antibody response.
Authors: Langley, D.B. / Schofield, P. / Nevoltris, D. / Jackson, J. / Jackson, K.J.L. / Peters, T.J. / Burk, M. / Matthews, J.M. / Basten, A. / Goodnow, C.C. / van Nunen, S. / Reed, J.H. / Christ, D.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJun 29, 2022ID: 6NUY
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 3, 2024Group: 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
L: M86 antibody Fab light chain
H: M86 antibody Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6485
Polymers49,1722
Non-polymers4763
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The two chains hold together over gel filtration chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-23 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.492, 101.492, 78.159
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-444-

HOH

21L-457-

HOH

31L-604-

HOH

41H-459-

HOH

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody M86 antibody Fab light chain


Mass: 24065.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody M86 antibody Fab heavy chain


Mass: 25106.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 349 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Equal volumes of a protein (in 25 mM Tris (pH 8.0), 100 mM NaCl) and well solution (1.5 M NaH2PO4.H2O.K2HPO4, pH 8.0) were combined.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→38.31 Å / Num. obs: 67630 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.021 / Rrim(I) all: 0.093 / Net I/σ(I): 17.2 / Num. measured all: 1276211 / Scaling rejects: 224
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.55-1.5814.31.7574750833190.4650.4751.8222.599.9
8.49-38.3115.90.05774194670.9980.0150.05945.499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.91 Å42.63 Å
Translation5.91 Å42.63 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: generic Fab

Resolution: 1.55→38.31 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.111 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0708 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 3288 4.9 %RANDOM
Rwork0.1276 ---
obs0.1298 64307 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.68 Å2 / Biso mean: 27.962 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.08 Å20 Å2
2--0.17 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 1.55→38.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 45 347 3588
Biso mean--24.81 39.79 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143128
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6444845
X-RAY DIFFRACTIONr_angle_other_deg1.4521.5827248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12922.887142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17815528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3511512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024548
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02800
X-RAY DIFFRACTIONr_rigid_bond_restr3.29636654
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 253 -
Rwork0.246 4694 -
all-4947 -
obs--99.82 %

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