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

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Basic information

Entry
Database: PDB / ID: 3llk
TitleSulfhydryl Oxidase Fragment of Human QSOX1
ComponentsSulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE / sulfhydryl oxidase / disulfide / flavin adenine dinucleotide / Alternative splicing / FAD / Flavoprotein / Glycoprotein / Golgi apparatus / Membrane / Polymorphism / Secreted / Transmembrane
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 / CITRATE ANION / Sulfhydryl oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfhydryl oxidase 1
B: Sulfhydryl oxidase 1
C: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9207
Polymers89,3743
Non-polymers2,5464
Water8,143452
1
A: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7663
Polymers29,7911
Non-polymers9752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5772
Polymers29,7911
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5772
Polymers29,7911
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.481, 161.573, 121.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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


Mass: 29791.412 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% (w/v) PEG 8000, 0.1 M citric acid, 10-15% ethanol, 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 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 56156 / Num. obs: 55492 / % possible obs: 98.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 5560 / Rsym value: 0.553 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LLI

3lli


Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 3928 -random
Rwork0.2372 ---
all-55971 --
obs-55254 98.7 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 172 452 6469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.006542
X-RAY DIFFRACTIONc_angle_deg2.18448

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