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- PDB-1bjx: HUMAN PROTEIN DISULFIDE ISOMERASE, NMR, 24 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bjx
TitleHUMAN PROTEIN DISULFIDE ISOMERASE, NMR, 24 STRUCTURES
ComponentsPROTEIN DISULFIDE ISOMERASEProtein disulfide-isomerase
KeywordsELECTRON TRANSPORT / REDOX-ACTIVE CENTER / ISOMERASE / ENDOPLASMIC RETICULUM
Function / homology
Function and homology information


regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline ...regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / endoplasmic reticulum chaperone complex / Chylomicron assembly / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / positive regulation of cell adhesion / protein-disulfide reductase activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / 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
Protein disulfide-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsKemmink, J. / Dijkstra, K. / Mariani, M. / Scheek, R.M. / Penka, E. / Nilges, M. / Darby, N.J.
Citation
Journal: J.Biomol.NMR / Year: 1999
Title: The structure in solution of the b domain of protein disulfide isomerase.
Authors: Kemmink, J. / Dijkstra, K. / Mariani, M. / Scheek, R.M. / Penka, E. / Nilges, M. / Darby, N.J.
#1: Journal: Curr.Biol. / Year: 1997
Title: The Folding Catalyst Protein Disulfide Isomerase is Constructed of Active and Inactive Thioredoxin Modules
Authors: Kemmink, J. / Darby, N.J. / Dijkstra, K. / Nilges, M. / Creighton, T.E.
History
DepositionJun 29, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN DISULFIDE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)12,0721
Polymers12,0721
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 100LOWEST ENERGY
Representative

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Components

#1: Protein PROTEIN DISULFIDE ISOMERASE / Protein disulfide-isomerase


Mass: 12072.295 Da / Num. of mol.: 1 / Fragment: B DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PET12A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07237, protein disulfide-isomerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY INOVAVarianUNITY INOVA6001
Bruker AMX600BrukerAMX6006002

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 24

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