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- PDB-3lli: Sulfhydryl Oxidase Fragment of Human QSOX1 -

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Basic information

Entry
Database: PDB / ID: 3lli
TitleSulfhydryl Oxidase Fragment of Human QSOX1
ComponentsSulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE / Sulfhydryl Oxidase / Flavin Adenine dinucleotide / disulfide / FAD / Flavoprotein / Glycoprotein / Golgi apparatus / Secreted
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / FAD binding / platelet alpha granule lumen / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / FAD binding / platelet alpha granule lumen / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / specific granule lumen / protein folding / Platelet degranulation / tertiary granule lumen / endoplasmic reticulum lumen / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
QSOX sulfhydryl oxidase domain / 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 / ERV/ALR sulfhydryl oxidase domain superfamily ...QSOX sulfhydryl oxidase domain / 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 / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Sulfhydryl oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsAlon, A. / Fass, D.
CitationJournal: Febs Lett. / Year: 2010
Title: QSOX contains a pseudo-dimer of functional and degenerate sulfhydryl oxidase domains.
Authors: Alon, A. / Heckler, E.J. / Thorpe, C. / Fass, D.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5772
Polymers29,7911
Non-polymers7861
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.606, 85.606, 125.706
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-695-

HOH

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Components

#1: Protein Sulfhydryl oxidase 1 / Oxidase / hQSOX / Quiescin Q6


Mass: 29791.412 Da / Num. of mol.: 1 / Fragment: UNP residues 286-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QSCN6, QSOX1, UNQ2520/PRO6013 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: O00391, thiol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12-16% (w/v) PEG 8000, 0.1M Citric acid, pH 5.3-5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 5.3-5.6

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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: Jul 11, 2008
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. all: 17773 / Num. obs: 17724 / % possible obs: 99.8 % / Redundancy: 16 % / Biso Wilson estimate: 43.8 Å2 / Rsym value: 0.056 / Net I/σ(I): 16.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1726 / Rsym value: 0.737 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.05→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3245 1207 -random
Rwork0.275 ---
all-17733 --
obs-17681 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 53 103 2178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.725

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