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- PDB-3wge: Crystal structure of ERp46 Trx2 -

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Basic information

Entry
Database: PDB / ID: 3wge
TitleCrystal structure of ERp46 Trx2
ComponentsThioredoxin 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 / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / protein-disulfide reductase activity / lysosomal lumen / azurophil granule lumen / protein folding / endoplasmic reticulum lumen ...Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein disulfide-isomerase / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / protein disulfide isomerase activity / protein-disulfide reductase activity / lysosomal lumen / azurophil granule lumen / protein folding / endoplasmic reticulum lumen / Neutrophil degranulation / negative regulation of apoptotic process / endoplasmic reticulum / extracellular exosome / extracellular region
Similarity search - Function
Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Disulphide isomerase / 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
Thioredoxin domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 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 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1002
Polymers13,0081
Non-polymers921
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.580, 39.060, 87.200
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 Thioredoxin domain-containing protein 5 / ERp46 / Endoplasmic reticulum resident protein 46 / ER protein 46 / Thioredoxin-like protein p46


Mass: 13007.667 Da / Num. of mol.: 1 / Fragment: Trx2 domain, UNP residues 190-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNDC5 / Plasmid: pOPTG / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)RIPL / References: UniProt: Q8NBS9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M HEPES, 2.2M Ammonium sulfate, pH 7.4, 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: 0.7 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 3, 2012
RadiationMonochromator: DIP-6040 Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.95→12.57 Å / Num. obs: 70957 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 6.85 Å2
Reflection shellResolution: 0.95→1 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→12.476 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.9475 / SU ML: 0.06 / σ(F): 1.39 / Phase error: 10.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1348 3579 5.05 %
Rwork0.1222 --
obs0.1228 70878 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.78 Å2 / Biso mean: 9.8302 Å2 / Biso min: 1.9 Å2
Refinement stepCycle: LAST / Resolution: 0.95→12.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms899 0 6 137 1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121244
X-RAY DIFFRACTIONf_angle_d1.371712
X-RAY DIFFRACTIONf_chiral_restr0.083163
X-RAY DIFFRACTIONf_plane_restr0.008234
X-RAY DIFFRACTIONf_dihedral_angle_d12.779489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.96250.23991310.218925722703100
0.9625-0.97570.21681280.195225502678100
0.9757-0.98960.20311510.184325402691100
0.9896-1.00440.20851250.168825722697100
1.0044-1.02010.16691350.155525542689100
1.0201-1.03680.15251240.143325612685100
1.0368-1.05460.13851350.132525832718100
1.0546-1.07380.14571630.119925212684100
1.0738-1.09450.13761460.105725482694100
1.0945-1.11680.10681370.099225812718100
1.1168-1.14110.11561340.093925392673100
1.1411-1.16760.11911560.09325792735100
1.1676-1.19680.1261260.093425672693100
1.1968-1.22910.10241200.091926032723100
1.2291-1.26520.12091290.095325982727100
1.2652-1.3060.1081250.091925992724100
1.306-1.35260.1191340.095425672701100
1.3526-1.40670.12561350.094125982733100
1.4067-1.47070.1141630.095925502713100
1.4707-1.54810.11241560.093926002756100
1.5481-1.64480.121300.093726202750100
1.6448-1.77150.12411320.100226122744100
1.7715-1.94920.11431420.106826332775100
1.9492-2.22980.13021480.113526322780100
2.2298-2.80410.14711250.13826972822100
2.8041-12.47670.14711490.16432723287297

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