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- PDB-2joo: The NMR Solution Structure of Recombinant RGD-hirudin -

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Basic information

Entry
Database: PDB / ID: 2joo
TitleThe NMR Solution Structure of Recombinant RGD-hirudin
ComponentsHirudin variant-1
KeywordsBLOOD CLOTTING / Mainly Beta
Function / homology
Function and homology information


negative regulation of serine-type peptidase activity / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Thrombin Inhibitor (Hirudin); Chain I / Thrombin Inhibitor (Hirudin), subunit I / Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHirudo medicinalis (medicinal leech)
MethodSOLUTION NMR / simulated annealing
AuthorsSong, X. / Mo, W. / Liu, X. / Yan, X. / Song, H. / Dai, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: The NMR solution structure of recombinant RGD-hirudin
Authors: Song, X. / Mo, W. / Liu, X. / Zhu, L. / Yan, X. / Song, H. / Dai, L.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hirudin variant-1


Theoretical massNumber of molelcules
Total (without water)7,0431
Polymers7,0431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60closest to the average
RepresentativeModel #1closest to the average

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Components

#1: Protein Hirudin variant-1 / Lepirudin


Mass: 7042.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Pichia pastoris (fungus) / References: UniProt: P01050

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

DetailsContents: 5 mM RGD-hirudin, 0.02mol/L Na2HPO4/NaH2PO4 buffer, pH 7.0, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 5 mM / Component: RGD-hirudin
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR softwareName: ARIA / Version: 2 / Developer: Linge, O'Donoghue and Nilges / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: closest to the average / Conformers calculated total number: 60 / Conformers submitted total number: 20

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