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- PDB-2j8l: FXI Apple 4 domain loop-out conformation -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2j8l
TitleFXI Apple 4 domain loop-out conformation
ComponentsCOAGULATION FACTOR XIFactor XI
KeywordsHYDROLASE / PROTEASE / GLYCOPROTEIN / POLYMORPHISM / SERINE PROTEASE / HEPARIN-BINDING / DISEASE MUTATION / FXI / BLOOD COAGULATION / PAN DOMAIN /APPLE DOMAIN / BLOOD COAGULATION / ALTERNATIVE SPLICING
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Hepatocyte Growth Factor / Hepatocyte Growth Factor / Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 3-Layer(bba) Sandwich / Serine proteases, trypsin family, histidine active site ...Hepatocyte Growth Factor / Hepatocyte Growth Factor / Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 3-Layer(bba) Sandwich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Coagulation factor XI
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CNS
AuthorsSamuel, D. / Cheng, H. / Riley, P.W. / Canutescu, A.A. / Bu, Z. / Walsh, P.N. / Roder, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Solution Structure of the A4 Domain of Factor Xi Sheds Light on the Mechanism of Zymogen Activation.
Authors: Samuel, D. / Cheng, H. / Riley, P.W. / Canutescu, A.A. / Nagaswami, C. / Weisel, J.W. / Bu, Z. / Walsh, P.N. / Roder, H.
History
DepositionOct 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAGULATION FACTOR XI
B: COAGULATION FACTOR XI


Theoretical massNumber of molelcules
Total (without water)19,9172
Polymers19,9172
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)14 / 1NO RESTRAINT VIOLATION AND LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein COAGULATION FACTOR XI / Factor XI / PLASMA THROMBOPLASTIN ANTECEDENT / PTA / FXI / FACTOR XI


Mass: 9958.274 Da / Num. of mol.: 2 / Fragment: APPLE 4 DOMAIN, RESIDUES 290-379 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P03951, coagulation factor XIa

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131HNHA
141CBCANH
151CBCA(CO)NH
NMR detailsText: SIDE-CHAIN ASSIGNMENTS WERE OBTAINED FROM 3D-15N TOCSY-HSQC AND 3D-HCCH-TOCSY . DISTANCE RESTRAINTS WERE OBTAINED FROM CROSS-PEAK VOLUMES IN 3D 15N NOESY-HSQC , 3D- 13C-EDITED NOESY AND HOMONUCLEAR NOESY

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionspH: 6.2 / Temperature: 310.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: CNS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATION AND LOWEST ENERGY
Conformers calculated total number: 1 / Conformers submitted total number: 14

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