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- PDB-9b76: Crystal structure of humanized 44H10 Fab Version 21 -

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Basic information

Entry
Database: PDB / ID: 9b76
TitleCrystal structure of humanized 44H10 Fab Version 21
Components
  • h44H10-V21 Antibody, heavy chain
  • h44H10-V21 Antibody, light chain
KeywordsIMMUNE SYSTEM / Antibody / Humanized
Function / homologyACETATE ION / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsKassardjian, A. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-148811 Canada
CitationJournal: Antibodies / Year: 2024
Title: Humanization of Pan-HLA-DR mAb 44H10 Hinges on Critical Residues in the Antibody Framework.
Authors: Kassardjian, A. / Ivanochko, D. / Barber, B. / Jetha, A. / Julien, J.P.
History
DepositionMar 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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
H: h44H10-V21 Antibody, heavy chain
L: h44H10-V21 Antibody, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,66213
Polymers47,2122
Non-polymers45011
Water5,332296
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.701, 86.068, 67.447
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody h44H10-V21 Antibody, heavy chain


Mass: 23717.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody h44H10-V21 Antibody, light chain


Mass: 23494.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M potassium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.73→40 Å / Num. obs: 41800 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.56 Å2 / CC1/2: 0.996 / Net I/σ(I): 13.2
Reflection shellResolution: 1.73→1.76 Å / Num. unique obs: 2076 / CC1/2: 0.583

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→35.87 Å / SU ML: 0.2373 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2117 2007 4.81 %
Rwork0.1753 39760 -
obs0.1771 41767 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.34 Å2
Refinement stepCycle: LAST / Resolution: 1.73→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 14 296 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943344
X-RAY DIFFRACTIONf_angle_d0.92014567
X-RAY DIFFRACTIONf_chiral_restr0.0609536
X-RAY DIFFRACTIONf_plane_restr0.0078574
X-RAY DIFFRACTIONf_dihedral_angle_d12.81261194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.39061400.31432799X-RAY DIFFRACTION99.22
1.77-1.820.27391440.25462841X-RAY DIFFRACTION99.24
1.82-1.870.26551420.23522783X-RAY DIFFRACTION98.42
1.87-1.940.29321440.22582853X-RAY DIFFRACTION99.34
1.94-20.23931440.18292795X-RAY DIFFRACTION99.59
2-2.080.24361390.18192862X-RAY DIFFRACTION99.54
2.08-2.180.20921430.17822887X-RAY DIFFRACTION99.64
2.18-2.290.2271410.18362833X-RAY DIFFRACTION99.56
2.29-2.440.20481450.17972851X-RAY DIFFRACTION99.83
2.44-2.630.23931440.18112789X-RAY DIFFRACTION97.83
2.63-2.890.20881470.18582858X-RAY DIFFRACTION99.83
2.89-3.310.17881400.17292871X-RAY DIFFRACTION99.93
3.31-4.170.19531470.15242857X-RAY DIFFRACTION99.4
4.17-35.870.18891470.15322881X-RAY DIFFRACTION98.66
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)
12.15869902608-0.282454521749-0.2376025031832.34017350614-0.526655728362.34207658559-0.0987006739812-0.1482250029650.1011912613850.03280851846970.07885199268950.1044125034280.0882341707105-0.03607499799511.851980529410.1459246226690.01122376271420.003540428192450.131525307679-0.01666268873530.187024290772-19.9984.6264.353
23.55944298472-1.079802074350.4005278972982.76099908509-0.3070655015833.31416469853-0.128054645349-0.6994080996760.04468016831790.1223764474060.18706680068-0.10647646485-0.5475322049680.255765502685-0.04056714402920.326902891869-0.0562971968318-0.02326851878070.428149364481-0.00888089000760.183784850444-8.734-11.95628.453
32.34128286764-1.327848774530.3621618515063.73055630865-0.6856590128791.14928459170.03903240595240.104333722636-0.0852810329821-0.225907156244-0.009495086377280.00055426814570.0135140765790.0096688283465-0.02629809816110.207030418105-0.02293609567430.006543262489640.153994693554-0.01984704601170.165318299165-11.12-12.679-6.869
41.66724289625-0.862259082658-0.9816759096461.62582249731.094567264584.46732813452-0.127543621721-0.639489969559-0.281805038980.2899424754720.1876970301470.2380674387410.3699914159020.0914082749055-0.05306114349340.242225579883-0.0029951150897-0.01776890116780.4375417542480.1146834420780.243848002285-13.391-27.71827.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:119 )H1 - 119
2X-RAY DIFFRACTION2( CHAIN H AND RESID 120:214 )H120 - 214
3X-RAY DIFFRACTION3( CHAIN L AND RESID 1:107 )L1 - 107
4X-RAY DIFFRACTION4( CHAIN L AND RESID 108:212 )L108 - 212

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