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- PDB-8ojv: Crystal structure of the human IgD Fab - structure Fab4 -

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Basic information

Entry
Database: PDB / ID: 8ojv
TitleCrystal structure of the human IgD Fab - structure Fab4
Components(Human IgD Fab ...) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody / Immunoglobulin
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 16, 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)49,16117
Polymers48,1692
Non-polymers99315
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint7 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.774, 71.645, 131.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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, 212 molecules

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


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: 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.: 197 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 18% PEG 8000 and 0.2M lithium sulphate

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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: 2.1→71.64 Å / Num. obs: 32773 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 37.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.05 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2634 / CC1/2: 0.627 / Rpim(I) all: 0.57

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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: 2.1→62.93 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 1632 5 %
Rwork0.1789 --
obs0.1808 32645 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→62.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 63 197 3602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033537
X-RAY DIFFRACTIONf_angle_d0.7054808
X-RAY DIFFRACTIONf_dihedral_angle_d12.4391268
X-RAY DIFFRACTIONf_chiral_restr0.047528
X-RAY DIFFRACTIONf_plane_restr0.004616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.29061330.27242533X-RAY DIFFRACTION100
2.16-2.230.29841360.24352560X-RAY DIFFRACTION100
2.23-2.310.29471340.23642559X-RAY DIFFRACTION100
2.31-2.40.26481320.23412515X-RAY DIFFRACTION100
2.4-2.510.28871350.21962550X-RAY DIFFRACTION100
2.51-2.650.27771340.22062563X-RAY DIFFRACTION100
2.65-2.810.25061360.22272562X-RAY DIFFRACTION100
2.81-3.030.26421360.20252589X-RAY DIFFRACTION100
3.03-3.330.20961330.18752567X-RAY DIFFRACTION100
3.33-3.820.22711390.17312621X-RAY DIFFRACTION100
3.82-4.810.16821390.13122630X-RAY DIFFRACTION100
4.81-62.930.16411450.14542764X-RAY DIFFRACTION100
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)
11.74370.5117-0.18441.2156-0.07641.11970.04980.0904-0.1357-0.00310.0829-0.1391-0.0612-0.0650.00010.21120.03790.02650.3263-0.00650.283310.6201-18.48961.8388
20.97150.5833-0.47331.2303-0.62610.4722-0.06250.1596-0.1412-0.04060.10330.0368-0.0453-0.027800.18910.01810.02320.3743-0.01550.28186.8799-17.44471.7692
30.524-0.4530.06110.07770.64781.6379-0.12880.15570.008-0.1323-0.05990.05040.0392-0.13560.00010.2894-0.01050.03650.22770.01010.260929.985-21.3468-26.4849
40.1443-0.37720.12010.8924-0.20710.7036-0.08010.39560.06750.2110.01490.07220.1598-0.0948-00.3078-0.01310.04010.3554-0.03350.324132.8933-21.3358-22.987
50.9334-0.4220.8390.92-0.02460.9230.01520.12240.00750.0347-0.0891-0.05140.10490.246200.3309-0.00080.06410.30960.04320.284738.4355-22.9078-31.7566
62.15830.8599-0.65631.91630.21021.56680.06840.0390.3110.13070.1140.162-0.4076-0.15630.00060.35910.08220.05310.30680.04780.343112.4582.4802-1.9846
70.4976-0.30350.03580.3125-0.22130.30050.0992-0.0253-0.07890.1424-0.0910.01720.10550.2495-0.00950.3493-0.12630.0380.24630.02550.238631.6054-3.5211-28.5867
81.1003-0.57-0.14472.1804-1.71131.22020.2011-0.0174-0.0694-0.2436-0.1707-0.09110.09430.06340.00070.3313-0.04380.0170.22960.0070.269426.5203-11.648-31.7849
90.1190.3355-0.10221.1631-1.14580.72540.24620.1143-0.0328-0.6199-0.17950.2634-0.2009-0.485400.44810.0126-0.04610.3035-0.00670.324823.1827-7.5906-39.3133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 2 through 50 )
2X-RAY DIFFRACTION2chain 'L' and (resid 51 through 105 )
3X-RAY DIFFRACTION3chain 'L' and (resid 106 through 155 )
4X-RAY DIFFRACTION4chain 'L' and (resid 156 through 176 )
5X-RAY DIFFRACTION5chain 'L' and (resid 177 through 217 )
6X-RAY DIFFRACTION6chain 'H' and (resid 2 through 119 )
7X-RAY DIFFRACTION7chain 'H' and (resid 120 through 134 )
8X-RAY DIFFRACTION8chain 'H' and (resid 135 through 191 )
9X-RAY DIFFRACTION9chain 'H' and (resid 192 through 224 )

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