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- PDB-2k8v: Solution structure of Oxidised ERp18 -

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Basic information

Entry
Database: PDB / ID: 2k8v
TitleSolution structure of Oxidised ERp18
ComponentsThioredoxin domain-containing protein 12
KeywordsOXIDOREDUCTASE / endoplasmic reticulum / thioredoxin fold / oxidase / Redox-active center
Function / homology
Function and homology information


protein-disulfide reductase (glutathione) / protein-disulfide reductase (glutathione) activity / protein-disulfide reductase activity / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
ERp19 / Thioredoxin-like / 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 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRowe, M.L. / Alanen, H.I. / Ruddock, L.W. / Kelly, G. / Schmidt, J.M. / Williamson, R.A. / Howard, M.J.
Citation
Journal: Biochemistry / Year: 2009
Title: Solution structure and dynamics of ERp18, a small endoplasmic reticulum resident oxidoreductase .
Authors: Rowe, M.L. / Ruddock, L.W. / Kelly, G. / Schmidt, J.M. / Williamson, R.A. / Howard, M.J.
#1: Journal: J. Biol. Chem. / Year: 2003
Title: Functional Characterization of ERp18, a New Endoplasmic Reticulum-located Thioredoxin Superfamily Member
Authors: Alanen, H.I. / Williamson, R.A. / Howard, M.J. / Lappi, A. / J ntti, H.P. / Rautio, S.M. / Kellokupu, S. / Ruddock, L.W.
History
DepositionSep 25, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin domain-containing protein 12


Theoretical massNumber of molelcules
Total (without water)17,8011
Polymers17,8011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Thioredoxin domain-containing protein 12 / Thioredoxin-like protein p19 / Endoplasmic reticulum protein ERp19 / ERp18 / hTLP19


Mass: 17800.961 Da / Num. of mol.: 1 / Fragment: UNP residues 24-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNDC12, TLP19, UNQ713/PRO1376 / Plasmid: pLysS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: O95881, protein-disulfide reductase (glutathione)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HN(CA)CB
1523D HBHA(CO)NH
1623D HBHANH
1723D HNCO
1823D C(CO)NH
1923D (H)CCH-TOCSY
11033D (H)CCH-TOCSY
11113D 1H-15N TOCSY
11213D 1H-15N NOESY
11323D 1H-13C NOESY
11543D CBCA(CO)NH
11643D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1.5 mM [U-99% 15N] ERp18, 20 mM sodium phosphate, 100 % sodium chloride, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21-1.5 mM [U-99% 13C; U-99% 15N] ERp18, 20 mM sodium phosphate, 100 % sodium chloride, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
30.7-1.5 mM [U-99% 13C; U-99% 15N] ERp18, 20 mM sodium phosphate, 100 % sodium chloride, 100 % D2O, 100% D2O100% D2O
40.7-1.5 mM [U-99% 13C; U-99% 15N] ERp18, 20 mM sodium phosphate, 100 % sodium chloride, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMERp18[U-99% 15N]1
20 mMsodium phosphate1
100 %sodium chloride1
10 %D2O1
1 mMERp18[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate2
100 %sodium chloride2
10 %D2O2
0.7 mMERp18[U-99% 13C; U-99% 15N]3
20 mMsodium phosphate3
100 %sodium chloride3
100 %D2O3
0.7 mMERp18[U-99% 13C; U-99% 15N]4
20 mMsodium phosphate4
100 %sodium chloride4
10 %D2O4
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
CCPN_AnalysisCCPNdata analysis
CCPN_AnalysisCCPNchemical shift assignment
CCPN_AnalysisCCPNpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
TALOSCornilescu, Delaglio and Baxgeometry optimization
TALOSCornilescu, Delaglio and Baxrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
ProcheckNMRLaskowski and MacArthurvalidation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2979 / NOE intraresidue total count: 1621 / NOE long range total count: 358 / NOE medium range total count: 358 / NOE sequential total count: 642 / Hydrogen bond constraints total count: 52
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 40
NMR ensemble rmsDistance rms dev: 0.0197 Å / Distance rms dev error: 0.0021 Å

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