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- PDB-8ojt: Crystal structure of the human IgD Fab - structure Fab2 -

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Basic information

Entry
Database: PDB / ID: 8ojt
TitleCrystal structure of the human IgD Fab - structure Fab2
Components(Human IgD Fab ...) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody / Immunoglobulin
Function / homologyAZIDE ION / NITRATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.1Oct 9, 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

Downloads & links

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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)48,95615
Polymers48,1692
Non-polymers78813
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-19 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.149, 73.827, 70.458
Angle α, β, γ (deg.)90.00, 92.54, 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 , 6 types, 349 molecules

#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BTP pH 6.5, 20% PEG 3350 and 0.2M sodium nitrate

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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: 1.55→70.39 Å / Num. obs: 64083 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 18.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.04 / Net I/σ(I): 10
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3165 / CC1/2: 0.486 / Rpim(I) all: 0.923 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→70.39 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 2970 4.64 %
Rwork0.1606 --
obs0.1623 63950 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→70.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 51 336 3708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073635
X-RAY DIFFRACTIONf_angle_d0.9415011
X-RAY DIFFRACTIONf_dihedral_angle_d12.691327
X-RAY DIFFRACTIONf_chiral_restr0.061565
X-RAY DIFFRACTIONf_plane_restr0.007647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.28951370.24482874X-RAY DIFFRACTION99
1.58-1.60.28011810.21572872X-RAY DIFFRACTION100
1.6-1.630.25371240.20962860X-RAY DIFFRACTION100
1.63-1.660.26741250.20652911X-RAY DIFFRACTION100
1.66-1.70.31751410.21542882X-RAY DIFFRACTION100
1.7-1.730.28331260.21932929X-RAY DIFFRACTION100
1.73-1.770.22571400.19962867X-RAY DIFFRACTION100
1.77-1.820.25741480.17162888X-RAY DIFFRACTION100
1.82-1.870.21441590.15962897X-RAY DIFFRACTION100
1.87-1.920.21571530.15582856X-RAY DIFFRACTION100
1.92-1.980.21581590.15562883X-RAY DIFFRACTION100
1.98-2.060.2181480.1632918X-RAY DIFFRACTION100
2.06-2.140.2111550.16722886X-RAY DIFFRACTION100
2.14-2.240.19451310.14972909X-RAY DIFFRACTION100
2.24-2.350.18221350.15272896X-RAY DIFFRACTION100
2.35-2.50.19971280.15982929X-RAY DIFFRACTION100
2.5-2.690.18021170.16462960X-RAY DIFFRACTION100
2.69-2.970.2021390.1642901X-RAY DIFFRACTION100
2.97-3.390.19671500.16142933X-RAY DIFFRACTION100
3.39-4.280.1591420.1422934X-RAY DIFFRACTION100
4.28-70.390.15931320.14172995X-RAY DIFFRACTION100

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