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- PDB-3t58: C76A/C455S mutant of mouse QSOX1 containing an interdomain disulfide -

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Basic information

Entry
Database: PDB / ID: 3t58
TitleC76A/C455S mutant of mouse QSOX1 containing an interdomain disulfide
ComponentsSulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE
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
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) / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Sulfhydryl oxidase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsFass, D. / Alon, A. / Gat, Y.
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
DepositionJul 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)235,5498
Polymers232,4074
Non-polymers3,1424
Water19,2941071
1
A: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8872
Polymers58,1021
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8872
Polymers58,1021
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)58,8872
Polymers58,1021
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8872
Polymers58,1021
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.871, 148.638, 215.789
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: 58101.789 Da / Num. of mol.: 4 / Fragment: UNP residues 36-550 / Mutation: C76A, C455S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qscn6, Qsox1, QSOX1b, Sox / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) plysS / References: UniProt: Q8BND5, thiol oxidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1071 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M MES monohydrate pH 6.5, 12% PEG 20K , VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2011
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 104870 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.114 / Rsym value: 0.144 / Net I/σ(I): 24.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.397 / % possible all: 98.9

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.4→50 Å / Occupancy max: 1 / Occupancy min: 0.37
RfactorNum. reflection% reflection
Rfree0.259 7254 6.9 %
Rwork0.2182 --
obs0.2182 103494 98.7 %
Solvent computationBsol: 42.7659 Å2
Displacement parametersBiso mean: 52.9811 Å2
Baniso -1Baniso -2Baniso -3
1-19.948 Å20 Å20 Å2
2---5.568 Å20 Å2
3----14.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15941 0 212 1071 17224
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3391.5
X-RAY DIFFRACTIONc_mcangle_it2.2432
X-RAY DIFFRACTIONc_scbond_it1.9252
X-RAY DIFFRACTIONc_scangle_it2.7972.5
LS refinement shellResolution: 2.4→2.42 Å /
RfactorNum. reflection
Rfree0.3601 90
Rwork0.295 -

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