- PDB-3uj1: Crystal structure of the third thioredoxin domain of human ERp46 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3uj1
Title
Crystal structure of the third thioredoxin domain of human ERp46
Components
Thioredoxin domain-containing protein 5
Keywords
CHAPERONE / Thioredoxin fold / Protein disulfide isomerase / Protein folding / Endoplasmic reticulum / substrate binding
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
Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Sequence details
ALTHOUGH THE FULL-LENGTH PROTEIN WAS USED IN THE CRYSTALLIZATION SETUP (SEE BELOW), AUTHORS SUSPECT ...ALTHOUGH THE FULL-LENGTH PROTEIN WAS USED IN THE CRYSTALLIZATION SETUP (SEE BELOW), AUTHORS SUSPECT THE CRYSTALLIZED PORTION DERIVED FROM PROTEOLYTIC CLEAVAGE IN THE CRYSTALLISATION TRIAL. THE ORIGIN OF THE PROTEASE IS UNCLEAR, ALSO THE PRECISE FRAGMENT SEQUENCE RESULTING FROM THE CLEAVAGE WAS NOT POSSIBLE TO ANALYZE IN DETAIL. SEQRES REMARK STARTS WITH THE CORRESPONDING MODELED COORDINATES. SDS-PAGE ANALYSIS REVEALED CLEAVAGE OF THE FULL-LENGTH PROTEIN IN TWO FRAGMENTS, COMPRISING TRX1-2 AND TRX3 DOMAINS. INITIAL POLYMERIC SEQUENCE USED FOR CRYSTALLIZATION (PRIOR TO LIMITED PROTEOLYSIS): MHHHHHHMRWGARAQEAAAAAADGPPAADGEDGQDPHSKHLYTADMFTHGIQSAAHFVMFF APWCGHCQRLQPTWNDLGDKYNSMEDAKVYVAKVDCTAHSDVCSAQGVRGYPTLKLFKPGQ EAVKYQGPRDFQTLENWMLQTLNEEPVTPEPEVEPPSAPELKQGLYELSASNFELHVAQGD HFIKFFAPWCGHCKALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWF RDGKKVDQYKGKRDLESLREYVESQLQRTETGATETVTPSEAPVLAAEPEADKGTVLALTE NNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSK YSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQAKDEL
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal grow
Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 20 % (w/v) PEG 10.000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Resolution: 2.651→55.062 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2522 / WRfactor Rwork: 0.2178 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7548 / SU B: 31.115 / SU ML: 0.261 / SU R Cruickshank DPI: 0.0988 / SU Rfree: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2591
239
4.9 %
RANDOM
Rwork
0.2287
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obs
0.2303
4841
98.27 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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