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- PDB-1g4g: NMR STRUCTURE OF THE FIFTH DOMAIN OF HUMAN BETA2-GLYCOPROTEIN I -

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Basic information

Entry
Database: PDB / ID: 1g4g
TitleNMR STRUCTURE OF THE FIFTH DOMAIN OF HUMAN BETA2-GLYCOPROTEIN I
ComponentsBETA2-GLYCOPROTEIN I
KeywordsSIGNALING PROTEIN / short consensus repeat / sushi-domain
Function / homology
Function and homology information


lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / chylomicron / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / very-low-density lipoprotein particle / negative regulation of blood coagulation ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / chylomicron / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / very-low-density lipoprotein particle / negative regulation of blood coagulation / high-density lipoprotein particle / negative regulation of endothelial cell migration / triglyceride metabolic process / plasminogen activation / negative regulation of endothelial cell proliferation / negative regulation of smooth muscle cell apoptotic process / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of angiogenesis / phospholipid binding / Platelet degranulation / heparin binding / collagen-containing extracellular matrix / lipid binding / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Beta-2-glycoprotein-1 fifth domain / Beta-2-glycoprotein-1 fifth domain / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Beta-2-glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsHoshino, M. / Hagihara, Y. / Nishii, I. / Yamazaki, T. / Kato, H. / Goto, Y.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Identification of the phospholipid-binding site of human beta(2)-glycoprotein I domain V by heteronuclear magnetic resonance.
Authors: Hoshino, M. / Hagihara, Y. / Nishii, I. / Yamazaki, T. / Kato, H. / Goto, Y.
History
DepositionOct 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA2-GLYCOPROTEIN I


Theoretical massNumber of molelcules
Total (without water)9,7551
Polymers9,7551
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)1 / -
Representativeminimized average structure

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Components

#1: Protein BETA2-GLYCOPROTEIN I


Mass: 9755.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P02749

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNCO-TROSY
141HMQC-J
151HNHB
161HN(CO)HB
171N15-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM beta2-glycoprotein I domain V U-15N; 20mM Na-phosphate buffer, pH 6.0; 90% H2O, 10% D2O90% H2O/10% D2O
21mM beta2-glycoprotein I domain V U-15N,13C; 20mM Na-phosphate buffer, pD 6.0; 100% D2O100% D2O
Sample conditionsIonic strength: 0.12 / pH: 6.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.841Brungerstructure solution
X-PLOR3.841Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1402 restraints, 1288 are NOE-derived distance constraints, 88 dihedral angle restraints, 26 distance restraints from hydrogen bonds
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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