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- PDB-3wgx: Crystal structure of ERp46 Trx2 in a complex with Prx4 C-term -

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Basic information

Entry
Database: PDB / ID: 3wgx
TitleCrystal structure of ERp46 Trx2 in a complex with Prx4 C-term
Components
  • Peroxiredoxin-4
  • Thioredoxin domain-containing protein 5
KeywordsISOMERASE / PDI family member / thioredoxin domain / protein disulfide isomerase
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein disulfide-isomerase / negative regulation of male germ cell proliferation / molecular sequestering activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / protein maturation by protein folding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity ...Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein disulfide-isomerase / negative regulation of male germ cell proliferation / molecular sequestering activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / protein maturation by protein folding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / smooth endoplasmic reticulum / protein-disulfide reductase activity / reactive oxygen species metabolic process / Neutrophil degranulation / extracellular matrix organization / lysosomal lumen / cell redox homeostasis / hydrogen peroxide catabolic process / male gonad development / azurophil granule lumen / protein folding / spermatogenesis / response to oxidative stress / molecular adaptor activity / endoplasmic reticulum lumen / Neutrophil degranulation / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / extracellular space / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Disulphide isomerase / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. ...Disulphide isomerase / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peroxiredoxin-4 / Thioredoxin domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.92 Å
AuthorsInaba, K. / Suzuki, M. / Kojima, R.
CitationJournal: Structure / Year: 2014
Title: Radically different thioredoxin domain arrangement of ERp46, an efficient disulfide bond introducer of the mammalian PDI family
Authors: Kojima, R. / Okumura, M. / Masui, S. / Kanemura, S. / Inoue, M. / Saiki, M. / Yamaguchi, H. / Hikima, T. / Suzuki, M. / Akiyama, S. / Inaba, K.
History
DepositionAug 13, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin domain-containing protein 5
B: Thioredoxin domain-containing protein 5
C: Peroxiredoxin-4
D: Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2285
Polymers30,1364
Non-polymers921
Water6,990388
1
A: Thioredoxin domain-containing protein 5
C: Peroxiredoxin-4


Theoretical massNumber of molelcules
Total (without water)15,0682
Polymers15,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-7 kcal/mol
Surface area6220 Å2
MethodPISA
2
B: Thioredoxin domain-containing protein 5
D: Peroxiredoxin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1603
Polymers15,0682
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-5 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.098, 36.406, 40.594
Angle α, β, γ (deg.)81.17, 87.47, 85.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thioredoxin domain-containing protein 5 / ERp46 / Endoplasmic reticulum resident protein 46 / ER protein 46 / Thioredoxin-like protein p46


Mass: 12975.602 Da / Num. of mol.: 2 / Fragment: Trx2 domain, UNP residues 190-298 / Mutation: C220A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLP46 / Plasmid: pOPTG / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)RIPL / References: UniProt: Q8NBS9
#2: Protein/peptide Peroxiredoxin-4 / / Prx4


Mass: 2092.330 Da / Num. of mol.: 2 / Fragment: c-term domain, UNP residues 244-263 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Mus musculus (house mouse) / References: UniProt: O08807
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 1.69 Å3/Da / Density % sol: 27.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1 M MES, 20% PEG3350 , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 17, 2013
RadiationMonochromator: DIP-6040 Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.92→26.785 Å / Num. obs: 126561 / % possible obs: 89.9 % / Redundancy: 2 % / Biso Wilson estimate: 7.86 Å2
Reflection shellResolution: 0.92→0.94 Å / % possible all: 62.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1386)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.92→26.785 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9281 / SU ML: 0.07 / σ(F): 1.97 / Phase error: 13.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.158 6367 5.03 %
Rwork0.1396 --
obs0.1405 126561 92.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 37.18 Å2 / Biso mean: 11.1088 Å2 / Biso min: 3.19 Å2
Refinement stepCycle: LAST / Resolution: 0.92→26.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 6 388 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132158
X-RAY DIFFRACTIONf_angle_d1.52945
X-RAY DIFFRACTIONf_chiral_restr0.101299
X-RAY DIFFRACTIONf_plane_restr0.01388
X-RAY DIFFRACTIONf_dihedral_angle_d13.217824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9204-0.93080.25871950.23063445364080
0.9308-0.94180.19441900.19113814400488
0.9418-0.95330.20882030.17663847405088
0.9533-0.96530.18661940.16433829402389
0.9653-0.97810.17342140.16133863407789
0.9781-0.99150.16761890.15053892408189
0.9915-1.00560.16422200.14093866408690
1.0056-1.02060.1542300.13273858408890
1.0206-1.03660.14622010.1233923412490
1.0366-1.05360.13882000.11583915411590
1.0536-1.07170.13092130.10813990420391
1.0717-1.09120.12462090.10443915412491
1.0912-1.11220.12822190.1053950416992
1.1122-1.13490.11742260.10154005423192
1.1349-1.15960.12461940.09954004419892
1.1596-1.18660.1172320.10223996422893
1.1866-1.21620.13821860.10474109429593
1.2162-1.24910.11822270.10934008423593
1.2491-1.28590.12781960.11634049424593
1.2859-1.32740.1442140.1244045425994
1.3274-1.37480.16541940.13554129432394
1.3748-1.42990.14212310.13544108433995
1.4299-1.49490.16562520.13754094434695
1.4949-1.57370.16592290.13554150437996
1.5737-1.67230.15551860.13894236442296
1.6723-1.80140.1522120.1424161437397
1.8014-1.98270.1642370.14874204444197
1.9827-2.26940.15232390.14524279451898
2.2694-2.85870.18722280.16654245447398
2.8587-26.79620.17362070.15064265447298

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