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- PDB-2k51: NMR Solution Structure of the Neurotrypsin Kringle Domain -

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Basic information

Entry
Database: PDB / ID: 2k51
TitleNMR Solution Structure of the Neurotrypsin Kringle Domain
ComponentsNeurotrypsin
KeywordsHYDROLASE / NEUROTRYPSIN / KRINGLE DOMAIN / DISULFIDE-RICH PROTEIN FOLD / SERINE ENDOPEPTIDASE / EXTRACELLULAR PROTEOLYSIS
Function / homology
Function and homology information


zymogen activation / exocytosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / synaptic cleft / Schaffer collateral - CA1 synapse / terminal bouton / peptidase activity / presynapse / cytoplasmic vesicle / axon ...zymogen activation / exocytosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / synaptic cleft / Schaffer collateral - CA1 synapse / terminal bouton / peptidase activity / presynapse / cytoplasmic vesicle / axon / serine-type endopeptidase activity / dendrite / synapse / glutamatergic synapse / proteolysis / plasma membrane
Similarity search - Function
SRCR domain signature. / Scavenger receptor cysteine-rich domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Kringle / Kringle, conserved site ...SRCR domain signature. / Scavenger receptor cysteine-rich domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / SRCR domain profile. / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SRCR domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Neurotrypsin / Neurotrypsin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsOzhogina, O.A.
CitationJournal: Biochemistry / Year: 2008
Title: NMR Solution Structure of the Neurotrypsin Kringle Domain
Authors: Ozhogina, O.A. / Grishaev, A. / Bominaar, E.L. / Llinas, M.
History
DepositionJun 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotrypsin


Theoretical massNumber of molelcules
Total (without water)8,5421
Polymers8,5421
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)1 / 70STRUCTURE WITH THE LOWEST RMSD TO THE MEAN COORDINATES OF THE ENSEMBLE
RepresentativeModel #1conformer with the lowest rmsd to the mean coordinates of the ensemble

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Components

#1: Protein Neurotrypsin


Mass: 8542.461 Da / Num. of mol.: 1
Fragment: KRINGLE DOMAIN, NT/K, sequence database residues 84-160
Source method: isolated from a genetically manipulated source
Details: FORMULA MASS: 8533 Da (NATURAL ABUNDANCE), 8635 Da (15N-ENRICHED), EXTINCTION COEFFICIENT (280 nm): 30855 M-1cm-1
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prss12, nt / Plasmid: pmed23 / Production host: Escherichia coli (E. coli) / Strain (production host): JM-109
References: UniProt: Q99JC8, UniProt: G3V801*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
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-15N HSQC
1212D [1H-15N]-HMBC
1312D 1H-13C HSQC
1412D 1H-1H COSY
1512D 1H-1H TOCSY
1612D 1H-1H NOESY
1713D TOCSY-[1H-15N]-HSQC
1813D NOESY-[1H-15N]-HSQC
1913D HNHA
11013D HNHB
NMR detailsText: CHEMICAL SHIFT REFERENCE: 1,4-DIOXANE, 3.75 PPM, SPECTRA USED FOR NOESY ASSIGNMENT AND STRUCTURE CALCULATIONS WERE: 2D [1H-1H]-NOESY (MIXING TIME OF 100 MS) AND 3D NOESY-[1H-15N]-HSQC (MIXING TIME OF 200 MS).

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Sample preparation

DetailsContents: 1 MM [U-100% 15N] NT/K, 0.02% sodium azide, 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Neurotrypsin / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: no salt / pH: 5.2 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
ARIA/CNS2LINGE, J., NILGES, M., HABECK, M., RIEPING, W.refinement
ARIA/CNS2LINGE, J., NILGES, M., HABECK, M., RIEPING, W.structure solution
BACUSstructure solution
CNS1.1structure solution
CcpNmr Analysis1.4structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE AUTOMATED NOESY ASSIGNMENT AND STRUCTURE CALCULATIONS CARRIED OUT BY BACUS/CNS. FINAL STRUCTURE REFINEMENT IN AN EXPLICIT SHELL OF WATER WAS PERFORMED USING ARIA/CNS, ON THE BASIS OF ...Details: THE AUTOMATED NOESY ASSIGNMENT AND STRUCTURE CALCULATIONS CARRIED OUT BY BACUS/CNS. FINAL STRUCTURE REFINEMENT IN AN EXPLICIT SHELL OF WATER WAS PERFORMED USING ARIA/CNS, ON THE BASIS OF FIXED UNAMBIGUOUS DISTANCE RESTRAINTS AND STRUCTURES OBTAINED WITH BACUS/CNS, AND RESTRAINTS ON DIHEDRAL ANGLES AND HYDROGEN BONDS. NOTE THAT RESIDUES 1 - 7 AT THE N-TERMINUS AND RESIDUES 73 - 77 AT THE C-TERMINUS ARE DISORDERED.
NMR constraintsNOE constraints total: 1342 / NOE intraresidue total count: 613 / NOE long range total count: 295 / NOE medium range total count: 119 / NOE sequential total count: 313 / Disulfide bond constraints total count: 3 / Hydrogen bond constraints total count: 24 / Protein chi angle constraints total count: 48 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 9
NMR representativeSelection criteria: conformer with the lowest rmsd to the mean coordinates of the ensemble
NMR ensembleConformer selection criteria: STRUCTURE WITH THE LOWEST RMSD TO THE MEAN COORDINATES OF THE ENSEMBLE
Conformers calculated total number: 70 / Conformers submitted total number: 1

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