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- PDB-2k13: Solution NMR Structure of the Leech Protein Saratin, a Novel Inhi... -

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Basic information

Entry
Database: PDB / ID: 2k13
TitleSolution NMR Structure of the Leech Protein Saratin, a Novel Inhibitor of Haemostasis
ComponentsSaratin
KeywordsTOXIN / collagen binding / mixed alpha/beta structure / fold typical for PAN domains
Function / homologyHepatocyte Growth Factor / Hepatocyte Growth Factor / 3-Layer(bba) Sandwich / Alpha Beta / Saratin
Function and homology information
Biological speciesHaementeria officinalis (Mexican leech)
MethodSOLUTION NMR / simulated annealing
AuthorsGronwald, W. / Bomke, J. / Maurer, T. / Wisotzki, B. / Huber, F. / Schumann, F. / Kremer, W. / Frech, M. / Kalbitzer, H.R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the leech protein saratin and characterization of its binding to collagen
Authors: Gronwald, W. / Bomke, J. / Maurer, T. / Domogalla, B. / Huber, F. / Schumann, F. / Kremer, W. / Fink, F. / Rysiok, T. / Frech, M. / Kalbitzer, H.R.
History
DepositionFeb 20, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Saratin


Theoretical massNumber of molelcules
Total (without water)12,0801
Polymers12,0801
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)10 / 100010 structure of lowest total and NOE energy
RepresentativeModel #1lowest total and noe energy

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Components

#1: Protein Saratin


Mass: 12079.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haementeria officinalis (Mexican leech) / References: UniProt: D0VWW8*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H NOESY
1223D 15N-separated NOESY
1343D 13C-separated NOESY
1422D 1H-15N HSQC
1532D 1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4-1.7 mM Saratin, 90% H2O/10% D2O90% H2O/10% D2O
21.4-1.7 mM [U-15N] Saratin, 90% H2O/10% D2O90% H2O/10% D2O
31.4-1.7 mM Saratin, 100% D2O100% D2O
41.4-1.7 mM [U-13C; U-15N] Saratin, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMSaratin1
1.4 mMSaratin[U-15N]2
1.4 mMSaratin3
1.4 mMSaratin[U-13C; U-15N]4
Sample conditionsIonic strength: 10 mM sodium phosphate buffer / pH: 6.5 / Pressure: ambient bar / Temperature: 298 K

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NMR measurement

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

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: refinement in explicit solvent (H2O)
NMR representativeSelection criteria: lowest total and noe energy
NMR ensembleConformer selection criteria: 10 structure of lowest total and NOE energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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