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- PDB-5d8i: Engineering the Species-Specificity of an Inhibitory Antibody Tar... -

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Basic information

Entry
Database: PDB / ID: 5d8i
TitleEngineering the Species-Specificity of an Inhibitory Antibody Targeting a Modulator of Tumor Stroma
ComponentsSulfhydryl oxidase 1
KeywordsOXIDOREDUCTASE / enzyme / disulfide bonds / thioredoxin fold
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 / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation ...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 / intercellular bridge / protein disulfide isomerase activity / Neutrophil degranulation / FAD binding / Golgi membrane / Golgi apparatus / endoplasmic reticulum / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfhydryl oxidase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGrossman, I. / Fass, D.
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 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 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 1.3Oct 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
A: Sulfhydryl oxidase 1
B: Sulfhydryl oxidase 1


Theoretical massNumber of molelcules
Total (without water)53,1842
Polymers53,1842
Non-polymers00
Water5,152286
1
A: Sulfhydryl oxidase 1


Theoretical massNumber of molelcules
Total (without water)26,5921
Polymers26,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfhydryl oxidase 1


Theoretical massNumber of molelcules
Total (without water)26,5921
Polymers26,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.480, 116.375, 50.023
Angle α, β, γ (deg.)90.00, 103.09, 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: 26591.994 Da / Num. of mol.: 2 / Fragment: UNP residues 36-275
Source method: isolated from a genetically manipulated source
Details: SVLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFA SWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLP GAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDL ...Details: SVLYSSSDPLTLLDADSVRPTVLGSSSAWAVEFFA SWCGHCIAFAPTWKELANDVKDWRPALNLAVLDCAEETNSAVCREFNIAGFPTVRFFQAFTKNGSGATLP GAGANVQTLRMRLIDALESHRDTWPPACPPLEPAKLNDIDGFFTRNKADYLALVFEREDSYLGREVTLDL SQYHAVAVRRVLNTESDLVNKFGVTDFPSCYLLLRNGSVSRVPVLVESRSFYTSYLRGLPGLTRD
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qsox1, Qscn6, Sox / Plasmid: pet15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BND5, thiol oxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.21 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 5% w/v dimethyl sulfoxide, 0.1 M sodium acetate, pH 4.6, 7% w/v PEG monomethyl ether 2 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: Aug 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 28528 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 11.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.2 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6O

3q6o


Resolution: 2.05→28.513 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1957 6.87 %random selection
Rwork0.201 ---
obs0.2045 28485 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 0 286 3993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063881
X-RAY DIFFRACTIONf_angle_d1.2755304
X-RAY DIFFRACTIONf_dihedral_angle_d11.91390
X-RAY DIFFRACTIONf_chiral_restr0.094592
X-RAY DIFFRACTIONf_plane_restr0.007698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0474-2.09860.31521050.27441556X-RAY DIFFRACTION78
2.0986-2.15530.28821120.2591765X-RAY DIFFRACTION89
2.1553-2.21870.32861430.25641821X-RAY DIFFRACTION92
2.2187-2.29030.28331330.24611872X-RAY DIFFRACTION95
2.2903-2.37210.29991650.22191893X-RAY DIFFRACTION97
2.3721-2.4670.28381380.22421916X-RAY DIFFRACTION98
2.467-2.57930.28681490.21191918X-RAY DIFFRACTION98
2.5793-2.71510.28591490.21141940X-RAY DIFFRACTION98
2.7151-2.88510.31151420.23371978X-RAY DIFFRACTION99
2.8851-3.10760.25741450.21051928X-RAY DIFFRACTION98
3.1076-3.41990.25211460.20991965X-RAY DIFFRACTION99
3.4199-3.91370.23931530.18231967X-RAY DIFFRACTION99
3.9137-4.92660.22041490.16061986X-RAY DIFFRACTION100
4.9266-28.51620.17791280.17462023X-RAY DIFFRACTION100

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