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- PDB-5d96: Oxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Frag... -

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Basic information

Entry
Database: PDB / ID: 5d96
TitleOxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Fragment from an Antibody Targeting Mouse and Human QSOX1
Components
  • Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1
  • Light chain of Fab fragment from an antibody targeting mouse and human QSOX1
  • Sulfhydryl oxidase 1
KeywordsIMMUNE SYSTEM / enzyme / inhibitor / antibody / dual-specificity
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / protein disulfide isomerase activity / Neutrophil degranulation / FAD binding ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Platelet degranulation / negative regulation of macroautophagy / protein disulfide isomerase activity / Neutrophil degranulation / FAD binding / Golgi membrane / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome
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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sulfhydryl oxidase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFass, D. / Grossman, I.
Funding support1items
OrganizationGrant numberCountry
European Research Council310649
CitationJournal: Protein Eng.Des.Sel. / Year: 2016
Title: Overcoming a species-specificity barrier in development of an inhibitory antibody targeting a modulator of tumor stroma.
Authors: Grossman, I. / Ilani, T. / Fleishman, S.J. / Fass, D.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Source and taxonomy
Revision 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Sulfhydryl oxidase 1
I: Light chain of Fab fragment from an antibody targeting mouse and human QSOX1
J: Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1
A: Sulfhydryl oxidase 1
B: Light chain of Fab fragment from an antibody targeting mouse and human QSOX1
C: Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1


Theoretical massNumber of molelcules
Total (without water)148,0186
Polymers148,0186
Non-polymers00
Water7,656425
1
D: Sulfhydryl oxidase 1
I: Light chain of Fab fragment from an antibody targeting mouse and human QSOX1
J: Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1


Theoretical massNumber of molelcules
Total (without water)74,0093
Polymers74,0093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-35 kcal/mol
Surface area28910 Å2
MethodPISA
2
A: Sulfhydryl oxidase 1
B: Light chain of Fab fragment from an antibody targeting mouse and human QSOX1
C: Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1


Theoretical massNumber of molelcules
Total (without water)74,0093
Polymers74,0093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-35 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.799, 204.770, 44.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sulfhydryl oxidase 1 / mSOx / Quiescin Q6 / Skin sulfhydryl oxidase


Mass: 27005.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qsox1, Qscn6, Sox / Plasmid: pet15b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8BND5, thiol oxidase
#2: Antibody Light chain of Fab fragment from an antibody targeting mouse and human QSOX1


Mass: 23551.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Heavy chain of Fab fragment from an antibody targeting mouse and human QSOX1


Mass: 23452.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM CaCl2, 0.1 M 2-(N-morpholino)ethanesulfonic acid buffer, pH 6, 22.5% w/v PEG 6 kD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 62461 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D8I, 4IJ3

5d8i

4ij3


Resolution: 2.3→27.424 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 2002 3.21 %random selection
Rwork0.1672 ---
obs0.1704 62422 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10170 0 0 425 10595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410436
X-RAY DIFFRACTIONf_angle_d1.01414199
X-RAY DIFFRACTIONf_dihedral_angle_d13.9093714
X-RAY DIFFRACTIONf_chiral_restr0.0361620
X-RAY DIFFRACTIONf_plane_restr0.0061815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.35740.31231440.24424346X-RAY DIFFRACTION96
2.3574-2.4210.33741370.23354234X-RAY DIFFRACTION97
2.421-2.49220.29271470.23654386X-RAY DIFFRACTION97
2.4922-2.57260.25221410.21534276X-RAY DIFFRACTION97
2.5726-2.66440.27221450.21754334X-RAY DIFFRACTION97
2.6644-2.7710.30811430.20874314X-RAY DIFFRACTION97
2.771-2.89690.29831380.19414278X-RAY DIFFRACTION97
2.8969-3.04930.27651480.184355X-RAY DIFFRACTION97
3.0493-3.240.27061410.17194331X-RAY DIFFRACTION97
3.24-3.48950.22291360.1654326X-RAY DIFFRACTION97
3.4895-3.83950.23641320.15454307X-RAY DIFFRACTION97
3.8395-4.39230.17391540.13224329X-RAY DIFFRACTION96
4.3923-5.52330.16351480.12254302X-RAY DIFFRACTION96
5.5233-24.47350.18181440.16414279X-RAY DIFFRACTION95

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