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- PDB-4p2l: Quiescin Sulfhydryl Oxidase from Rattus norvegicus -

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Basic information

Entry
Database: PDB / ID: 4p2l
TitleQuiescin Sulfhydryl Oxidase from Rattus norvegicus
ComponentsSulfhydryl oxidase 1Oxidase
KeywordsOXIDOREDUCTASE / Disulfide formation / Enzyme intermediate / Thioredoxin fold / Erv fold
Function / homology
Function and homology information


: / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Neutrophil degranulation / negative regulation of macroautophagy / intercellular bridge ...: / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / flavin-dependent sulfhydryl oxidase activity / thiol oxidase / extracellular matrix assembly / Neutrophil degranulation / negative regulation of macroautophagy / intercellular bridge / protein disulfide isomerase activity / FAD binding / protein folding / Golgi membrane / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Sulfhydryl oxidase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGat, Y. / Fass, D.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation593/08 Israel
CitationJournal: Protein Sci. / Year: 2014
Title: Enzyme structure captures four cysteines aligned for disulfide relay.
Authors: Gat, Y. / Vardi-Kilshtain, A. / Grossman, I. / Major, D.T. / Fass, D.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Derived calculations
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.6Sep 27, 2023Group: 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 / refine_hist
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
B: Sulfhydryl oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1764
Polymers113,6052
Non-polymers1,5712
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-17 kcal/mol
Surface area41520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.495, 169.583, 68.369
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Sulfhydryl oxidase 1 / Oxidase / rSOx / FAD-dependent sulfhydryl oxidase-2 / SOx-2 / Quiescin Q6


Mass: 56802.660 Da / Num. of mol.: 2 / Fragment: UNP residues 27-544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Qsox1, Qscn6, Sox2 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6IUU3, thiol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M sodium citrate buffer, pH 6.0, 0.25 M NaCl, 27% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→48.78 Å / Num. obs: 25595 / % possible obs: 99.89 % / Redundancy: 4.6 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.149 / Net I/σ(I): 10.6
Reflection shellResolution: 2.9→2.96 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
SCALEPACKdata scaling
PHASERphasing
CNS1.3refinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T58

3t58


Resolution: 2.9→48.78 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1759 6.87 %Random selection
Rwork0.178 ---
obs0.182 25589 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7875 0 106 222 8203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038256
X-RAY DIFFRACTIONf_angle_d0.68611245
X-RAY DIFFRACTIONf_dihedral_angle_d11.5332954
X-RAY DIFFRACTIONf_chiral_restr0.0461212
X-RAY DIFFRACTIONf_plane_restr0.0031435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97840.34071630.23581788X-RAY DIFFRACTION100
2.9784-3.06610.36011280.21341779X-RAY DIFFRACTION100
3.0661-3.1650.29871240.21071816X-RAY DIFFRACTION100
3.165-3.27810.25111380.18611807X-RAY DIFFRACTION100
3.2781-3.40930.24531260.19261823X-RAY DIFFRACTION100
3.4093-3.56450.26311320.18011817X-RAY DIFFRACTION100
3.5645-3.75230.2651430.16481799X-RAY DIFFRACTION100
3.7523-3.98730.22611290.17131833X-RAY DIFFRACTION100
3.9873-4.2950.20311300.15311828X-RAY DIFFRACTION100
4.295-4.72690.22831390.15321830X-RAY DIFFRACTION100
4.7269-5.41010.21841400.15961859X-RAY DIFFRACTION100
5.4101-6.81320.22871330.19481886X-RAY DIFFRACTION100
6.8132-48.78160.17851340.17381965X-RAY DIFFRACTION99

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