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- PDB-5d93: Oxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Frag... -

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Basic information

Entry
Database: PDB / ID: 5d93
TitleOxidoreductase Fragment of Mouse QSOX1 in Complex with a FAb Fragment from a Mouse QSOX1-Specific Antibody
Components
  • Heavy Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody
  • Light Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody
  • Sulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE / enzyme / inhibitor / thioredoxin fold / antibody
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 / protein folding / Golgi membrane / intracellular membrane-bounded organelle / 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 / 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: 2.201 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 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Feb 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 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfhydryl oxidase 1
C: Heavy Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody
B: Light Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody
D: Sulfhydryl oxidase 1
F: Heavy Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody
E: Light Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody


Theoretical massNumber of molelcules
Total (without water)147,2496
Polymers147,2496
Non-polymers00
Water13,529751
1
A: Sulfhydryl oxidase 1
C: Heavy Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody
B: Light Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody


Theoretical massNumber of molelcules
Total (without water)73,6243
Polymers73,6243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Sulfhydryl oxidase 1
F: Heavy Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody
E: Light Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody


Theoretical massNumber of molelcules
Total (without water)73,6243
Polymers73,6243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.539, 112.715, 193.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27005.467 Da / Num. of mol.: 2 / Fragment: residues 36-275
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 Heavy Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody


Mass: 23428.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): epethelial / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Antibody Light Chain of Fab Fragment from a Mouse QSOX1-Specific Antibody


Mass: 23190.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): epethelial / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 751 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM ammonium sulfate, 0.1 M bis-tris methane buffer, pH 5.5, 22% w/v PEG 3.35 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: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 72630 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D8I, 3D85, 4Q0X, 3AB0

5d8i

3d85

4q0x

3ab0


Resolution: 2.201→23.203 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 3588 4.94 %random selection
Rwork0.174 ---
obs0.1771 72573 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.65 Å2
Refinement stepCycle: LAST / Resolution: 2.201→23.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10156 0 0 751 10907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810430
X-RAY DIFFRACTIONf_angle_d1.11314201
X-RAY DIFFRACTIONf_dihedral_angle_d13.3493691
X-RAY DIFFRACTIONf_chiral_restr0.0411588
X-RAY DIFFRACTIONf_plane_restr0.0051809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2012-2.23020.28871100.21032462X-RAY DIFFRACTION94
2.2302-2.26070.28511360.20722687X-RAY DIFFRACTION100
2.2607-2.2930.29721280.21172625X-RAY DIFFRACTION100
2.293-2.32720.26441470.21092653X-RAY DIFFRACTION100
2.3272-2.36350.29181500.2072625X-RAY DIFFRACTION100
2.3635-2.40220.30041380.20882661X-RAY DIFFRACTION100
2.4022-2.44360.27641400.20692644X-RAY DIFFRACTION100
2.4436-2.4880.28911120.20642660X-RAY DIFFRACTION100
2.488-2.53580.27511320.19572679X-RAY DIFFRACTION100
2.5358-2.58750.27511620.19622628X-RAY DIFFRACTION100
2.5875-2.64370.25871440.19612662X-RAY DIFFRACTION100
2.6437-2.70510.25351510.19512655X-RAY DIFFRACTION100
2.7051-2.77260.31881320.19422650X-RAY DIFFRACTION100
2.7726-2.84740.25421260.1912716X-RAY DIFFRACTION100
2.8474-2.93110.27281430.19912632X-RAY DIFFRACTION100
2.9311-3.02550.26281440.19512672X-RAY DIFFRACTION100
3.0255-3.13340.25641470.20162689X-RAY DIFFRACTION100
3.1334-3.25850.2431260.19182685X-RAY DIFFRACTION100
3.2585-3.40640.24561330.18492679X-RAY DIFFRACTION100
3.4064-3.58530.23051600.17042654X-RAY DIFFRACTION99
3.5853-3.80910.20261350.16652675X-RAY DIFFRACTION99
3.8091-4.10170.19041390.14932685X-RAY DIFFRACTION98
4.1017-4.51170.2031420.12982649X-RAY DIFFRACTION98
4.5117-5.15830.18661550.12892627X-RAY DIFFRACTION97
5.1583-6.47540.18151220.15072666X-RAY DIFFRACTION95
6.4754-23.20420.22331340.14912665X-RAY DIFFRACTION92

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