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- PDB-3q6o: Oxidoreductase Fragment of Human QSOX1 -

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Basic information

Entry
Database: PDB / ID: 3q6o
TitleOxidoreductase Fragment of Human QSOX1
ComponentsSulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE / protein disulfide isomerase / thioredoxin / Thioredoxin fold / reductive methylation
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
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsFass, D. / Alon, A.
CitationJournal: Nature / Year: 2012
Title: The dynamic disulphide relay of quiescin sulphydryl oxidase.
Authors: Alon, A. / Grossman, I. / Gat, Y. / Kodali, V.K. / DiMaio, F. / Mehlman, T. / Haran, G. / Baker, D. / Thorpe, C. / Fass, D.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5205
Polymers27,1361
Non-polymers3844
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.170, 65.250, 68.560
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 / hQSOX / Quiescin Q6


Mass: 27135.908 Da / Num. of mol.: 1 / Fragment: UNP residues 33-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QSCN6, QSOX1, QSOX1a, UNQ2520/PRO6013 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: O00391, thiol oxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% w/v PEG 3350, 0.2 M lithium sulfate monohydrate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 8, 2010
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: 16408 / Num. obs: 16404 / % possible obs: 100 % / Redundancy: 5.3 % / Rsym value: 0.082 / Net I/σ(I): 8.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2363 / % possible all: 100

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Processing

Software
NameClassification
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.05→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2613 825 5 %
Rwork0.2017 15486 -
obs-16311 99.7 %
Solvent computationBsol: 56.1332 Å2
Displacement parametersBiso max: 94.41 Å2 / Biso mean: 25.9358 Å2 / Biso min: 10.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.971 Å20 Å20 Å2
2---1.16 Å20 Å2
3----0.811 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 20 239 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2881.5
X-RAY DIFFRACTIONc_scbond_it2.0752
X-RAY DIFFRACTIONc_mcangle_it1.9522
X-RAY DIFFRACTIONc_scangle_it3.0232.5

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