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- PDB-8aon: Oxidoreductase fragment of human QSOX1 in complex with a Fab frag... -

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Basic information

Entry
Database: PDB / ID: 8aon
TitleOxidoreductase fragment of human QSOX1 in complex with a Fab fragment of a humanized anti-QSOX1 antibody
Components
  • Heavy chain
  • Light chain
  • Oxidoreductase fragment of human QSOX1
KeywordsIMMUNE SYSTEM / antibody / humanized / Fab / QSOX1
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / protein disulfide isomerase activity / protein folding / extracellular space
Similarity search - Function
Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain / Sulfhydryl oxidase, Trx-like domain / Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain superfamily / QSOX Trx-like domain / Flavin adenine dinucleotide (FAD)-dependent sulfhydryl oxidase / Sulfhydryl oxidase / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. ...Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain / Sulfhydryl oxidase, Trx-like domain / Sulfhydryl oxidase, flavin adenine dinucleotide (FAD) binding domain superfamily / QSOX Trx-like domain / Flavin adenine dinucleotide (FAD)-dependent sulfhydryl oxidase / Sulfhydryl oxidase / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhmelnitsky, L. / Fass, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)825076European Union
CitationJournal: Nat Biomed Eng / Year: 2024
Title: Computational optimization of antibody humanness and stability by systematic energy-based ranking.
Authors: Tennenhouse, A. / Khmelnitsky, L. / Khalaila, R. / Yeshaya, N. / Noronha, A. / Lindzen, M. / Makowski, E.K. / Zaretsky, I. / Sirkis, Y.F. / Galon-Wolfenson, Y. / Tessier, P.M. / Abramson, J. ...Authors: Tennenhouse, A. / Khmelnitsky, L. / Khalaila, R. / Yeshaya, N. / Noronha, A. / Lindzen, M. / Makowski, E.K. / Zaretsky, I. / Sirkis, Y.F. / Galon-Wolfenson, Y. / Tessier, P.M. / Abramson, J. / Yarden, Y. / Fass, D. / Fleishman, S.J.
History
DepositionAug 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 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
Revision 1.2Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B00A: Oxidoreductase fragment of human QSOX1
B: Heavy chain
C: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3614
Polymers74,2693
Non-polymers921
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-38 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.168, 98.721, 63.090
Angle α, β, γ (deg.)90.000, 101.190, 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: Protein Oxidoreductase fragment of human QSOX1


Mass: 27000.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A8K4C2
#2: Antibody Heavy chain


Mass: 23851.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-F / Production host: Homo sapiens (human)
#3: Antibody Light chain


Mass: 23417.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-F / Production host: Homo sapiens (human)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium phosphate dibasic

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→49.36 Å / Num. obs: 102949 / % possible obs: 97 % / Redundancy: 2.7 % / Biso Wilson estimate: 46.08 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.075 / Net I/σ(I): 6.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.82 % / Num. unique obs: 3817 / Rpim(I) all: 1.127 / % possible all: 98.55

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IJ3

4ij3


Resolution: 2.1→49.36 Å / SU ML: 0.3429 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 31.4747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 7728 10 %
Rwork0.1978 69556 -
obs0.2039 77284 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 6 211 5222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00735196
X-RAY DIFFRACTIONf_angle_d0.90837096
X-RAY DIFFRACTIONf_chiral_restr0.0552798
X-RAY DIFFRACTIONf_plane_restr0.0081920
X-RAY DIFFRACTIONf_dihedral_angle_d7.2952740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.43182540.3692257X-RAY DIFFRACTION99.8
2.12-2.150.41132600.34382373X-RAY DIFFRACTION99.81
2.15-2.180.37832610.31972349X-RAY DIFFRACTION99.92
2.18-2.20.32242520.31652270X-RAY DIFFRACTION99.96
2.2-2.230.35732620.2992352X-RAY DIFFRACTION99.73
2.23-2.260.33522530.29412312X-RAY DIFFRACTION99.96
2.26-2.290.37512640.29032368X-RAY DIFFRACTION99.96
2.29-2.330.32912540.28382301X-RAY DIFFRACTION99.73
2.33-2.370.38442610.26682326X-RAY DIFFRACTION99.88
2.37-2.40.28832570.27492334X-RAY DIFFRACTION99.88
2.4-2.450.30532640.24962347X-RAY DIFFRACTION99.81
2.45-2.490.29942550.2452275X-RAY DIFFRACTION99.8
2.49-2.540.32452630.23882356X-RAY DIFFRACTION99.73
2.54-2.590.3152510.24352264X-RAY DIFFRACTION99.76
2.59-2.650.32992650.23742356X-RAY DIFFRACTION99.51
2.65-2.710.28722620.23582339X-RAY DIFFRACTION99.88
2.71-2.770.31922540.2362306X-RAY DIFFRACTION99.84
2.78-2.850.35222550.22942304X-RAY DIFFRACTION99.88
2.85-2.930.30652570.23852333X-RAY DIFFRACTION99.73
2.93-3.030.29322610.22812330X-RAY DIFFRACTION99.92
3.03-3.140.29472540.23482318X-RAY DIFFRACTION99.54
3.14-3.260.30232600.21412313X-RAY DIFFRACTION99.23
3.26-3.410.30312550.21242306X-RAY DIFFRACTION99.42
3.41-3.590.31142570.20012290X-RAY DIFFRACTION99.3
3.59-3.820.23032620.17912328X-RAY DIFFRACTION99.2
3.82-4.110.19062540.16232305X-RAY DIFFRACTION99.19
4.11-4.520.20322510.14972327X-RAY DIFFRACTION99.12
4.52-5.180.20222550.13532309X-RAY DIFFRACTION98.92
5.18-6.520.18472560.16122313X-RAY DIFFRACTION99.5
6.52-49.360.20042590.14942295X-RAY DIFFRACTION98.8

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