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- PDB-6hf1: Mutant oxidoreductase fragment of mouse QSOX1 in complex with an ... -

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Basic information

Entry
Database: PDB / ID: 6hf1
TitleMutant oxidoreductase fragment of mouse QSOX1 in complex with an antibody Fab
Components
  • (Fab 316 heavy chain) x 2
  • Fab 316 light chain
  • Sulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE / disulfide bond / cis-proline / thioredoxin
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsGrossman-Haham, I. / Fass, D.
Funding support1items
OrganizationGrant numberCountry
European Research Council310649
CitationJournal: Protein Sci. / Year: 2019
Title: cis-Proline mutants of quiescin sulfhydryl oxidase 1 with altered redox properties undermine extracellular matrix integrity and cell adhesion in fibroblast cultures.
Authors: Javitt, G. / Grossman-Haham, I. / Alon, A. / Resnick, E. / Mutsafi, Y. / Ilani, T. / Fass, D.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Fab 316 heavy chain
B: Fab 316 light chain
D: Sulfhydryl oxidase 1
F: Fab 316 heavy chain
E: Fab 316 light chain


Theoretical massNumber of molelcules
Total (without water)145,1756
Polymers145,1756
Non-polymers00
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13320 Å2
ΔGint-71 kcal/mol
Surface area53410 Å2
MethodPISA
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: 26326.746 Da / Num. of mol.: 2 / Mutation: C75A, P122T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qsox1, Qscn6, Sox / Production host: Escherichia coli (E. coli) / References: UniProt: Q8BND5, thiol oxidase
#2: Antibody Fab 316 heavy chain


Mass: 23108.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Fab 316 light chain


Mass: 23087.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Antibody Fab 316 heavy chain


Mass: 23237.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M sodium citrate, pH 6.0 16% w/v PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.937→98 Å / Num. obs: 104667 / % possible obs: 97.6 % / Redundancy: 2.3 % / Net I/σ(I): 13.7
Reflection shellResolution: 1.94→2.02 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8728 / % possible all: 82.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D93

5d93


Resolution: 1.94→48.886 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.231 5215 4.98 %
Rwork0.1937 --
obs0.1956 104667 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.94→48.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10105 0 0 804 10909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710426
X-RAY DIFFRACTIONf_angle_d0.88214230
X-RAY DIFFRACTIONf_dihedral_angle_d5.0168000
X-RAY DIFFRACTIONf_chiral_restr0.0521592
X-RAY DIFFRACTIONf_plane_restr0.0061814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9371-1.95910.341840.29921597X-RAY DIFFRACTION48
1.9591-1.98210.30191770.28723384X-RAY DIFFRACTION100
1.9821-2.00630.3161750.2783311X-RAY DIFFRACTION100
2.0063-2.03170.33221750.27293347X-RAY DIFFRACTION100
2.0317-2.05840.32491770.25963367X-RAY DIFFRACTION100
2.0584-2.08660.30011760.25623351X-RAY DIFFRACTION100
2.0866-2.11640.29381750.24823341X-RAY DIFFRACTION100
2.1164-2.1480.31071760.25073331X-RAY DIFFRACTION100
2.148-2.18160.28671770.24873382X-RAY DIFFRACTION100
2.1816-2.21740.31711820.23933337X-RAY DIFFRACTION100
2.2174-2.25560.30011810.2383366X-RAY DIFFRACTION100
2.2556-2.29660.28011870.23313333X-RAY DIFFRACTION100
2.2966-2.34080.31071810.23033373X-RAY DIFFRACTION100
2.3408-2.38860.2611750.22673316X-RAY DIFFRACTION100
2.3886-2.44050.29251660.2313386X-RAY DIFFRACTION99
2.4405-2.49730.28691740.23083362X-RAY DIFFRACTION99
2.4973-2.55970.271810.22983353X-RAY DIFFRACTION100
2.5597-2.62890.27651550.21573409X-RAY DIFFRACTION100
2.6289-2.70630.26041920.22043343X-RAY DIFFRACTION100
2.7063-2.79360.25981770.2143375X-RAY DIFFRACTION99
2.7936-2.89350.26941660.21263390X-RAY DIFFRACTION99
2.8935-3.00930.25751700.21783370X-RAY DIFFRACTION99
3.0093-3.14620.29591930.2083356X-RAY DIFFRACTION99
3.1462-3.31210.23561580.1913386X-RAY DIFFRACTION99
3.3121-3.51950.21950.18283360X-RAY DIFFRACTION99
3.5195-3.79120.19331570.17473388X-RAY DIFFRACTION98
3.7912-4.17250.17251820.15593390X-RAY DIFFRACTION98
4.1725-4.77580.15811750.13993392X-RAY DIFFRACTION98
4.7758-6.01530.18992000.1553456X-RAY DIFFRACTION99
6.0153-48.90130.2021760.17283600X-RAY DIFFRACTION98

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