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- PDB-8oju: Crystal structure of the human IgD Fab - structure Fab3 -

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Basic information

Entry
Database: PDB / ID: 8oju
TitleCrystal structure of the human IgD Fab - structure Fab3
Components(Human IgD Fab ...) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody / Immunoglobulin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDavies, A.M. / Beavil, R.L. / McDonnell, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V010557/1 United Kingdom
CitationJournal: Mol.Immunol. / Year: 2023
Title: Crystal structures of the human IgD Fab reveal insights into C H 1 domain diversity.
Authors: Davies, A.M. / Beavil, R.L. / Barbolov, M. / Sandhar, B.S. / Gould, H.J. / Beavil, A.J. / Sutton, B.J. / McDonnell, J.M.
History
DepositionMar 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Human IgD Fab light chain
H: Human IgD Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,96714
Polymers48,1692
Non-polymers79912
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-10 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.893, 74.198, 70.915
Angle α, β, γ (deg.)90.00, 92.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Human IgD Fab light chain


Mass: 22769.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVitro / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Human IgD Fab heavy chain


Mass: 25399.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVitro / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 397 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 6000 and 0.1M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 1.45→70.87 Å / Num. obs: 78636 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 11.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3890 / CC1/2: 0.462 / Rpim(I) all: 0.661 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→51.25 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 3928 5 %
Rwork0.1568 --
obs0.1585 78598 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→51.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 48 385 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073651
X-RAY DIFFRACTIONf_angle_d0.9325030
X-RAY DIFFRACTIONf_dihedral_angle_d12.6171354
X-RAY DIFFRACTIONf_chiral_restr0.09569
X-RAY DIFFRACTIONf_plane_restr0.007648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.30591400.27992633X-RAY DIFFRACTION100
1.47-1.490.29671430.24482689X-RAY DIFFRACTION100
1.49-1.510.27291370.2232642X-RAY DIFFRACTION100
1.51-1.530.26941480.20732645X-RAY DIFFRACTION100
1.53-1.550.25781240.19762648X-RAY DIFFRACTION100
1.55-1.570.20951430.17382677X-RAY DIFFRACTION100
1.57-1.60.23121430.17752666X-RAY DIFFRACTION100
1.6-1.620.2341360.16662645X-RAY DIFFRACTION100
1.62-1.650.21931410.17392701X-RAY DIFFRACTION100
1.65-1.680.22591390.16572614X-RAY DIFFRACTION100
1.68-1.710.23151420.17562675X-RAY DIFFRACTION100
1.71-1.750.2091260.18922650X-RAY DIFFRACTION100
1.75-1.790.26081460.16512675X-RAY DIFFRACTION100
1.79-1.830.2131440.15542646X-RAY DIFFRACTION100
1.83-1.870.21181300.14072661X-RAY DIFFRACTION100
1.87-1.920.17031490.13542642X-RAY DIFFRACTION100
1.92-1.980.18061350.13752672X-RAY DIFFRACTION100
1.98-2.040.15421460.14822681X-RAY DIFFRACTION100
2.04-2.120.17291350.15242650X-RAY DIFFRACTION100
2.12-2.20.21221370.14812680X-RAY DIFFRACTION100
2.2-2.30.1891370.1512654X-RAY DIFFRACTION100
2.3-2.420.19441530.15432674X-RAY DIFFRACTION100
2.42-2.570.18591370.15832670X-RAY DIFFRACTION100
2.57-2.770.20291400.16192673X-RAY DIFFRACTION100
2.77-3.050.19411490.15852692X-RAY DIFFRACTION100
3.05-3.490.17921460.15632658X-RAY DIFFRACTION100
3.49-4.40.15141390.13922715X-RAY DIFFRACTION100
4.4-51.250.1641430.15142742X-RAY DIFFRACTION100

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