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- PDB-2ike: Solution Structure of the second Clip domain in PAP2 -

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Basic information

Entry
Database: PDB / ID: 2ike
TitleSolution Structure of the second Clip domain in PAP2
ComponentsProphenoloxidase activating proteinase-2
KeywordsHYDROLASE / BETA-SHEET / DOUBLE HELIX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
mini-chromosome maintenance (MCM) complex, chain A, domain 1 - #30 / Proteinase, regulatory CLIP domain superfamily / Regulatory CLIP domain of proteinases / Clip or disulphide knot domain / Proteinase, regulatory CLIP domain / Clip domain profile. / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...mini-chromosome maintenance (MCM) complex, chain A, domain 1 - #30 / Proteinase, regulatory CLIP domain superfamily / Regulatory CLIP domain of proteinases / Clip or disulphide knot domain / Proteinase, regulatory CLIP domain / Clip domain profile. / mini-chromosome maintenance (MCM) complex, chain A, domain 1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CLIP domain-containing serine protease / CLIP domain-containing serine protease
Similarity search - Component
Biological speciesManduca sexta (tobacco hornworm)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
AuthorsHuang, R.D. / Lv, Z.Q. / Dai, H.E. / Velde, D.V. / Prakash, O. / Jiang, H.B.
CitationJournal: To be Published
Title: Solution structure of Clip domain in PAP2
Authors: Huang, R.D. / Lv, Z.Q. / Dai, H.E. / Velde, D.V. / Prakash, O. / Jiang, H.B.
History
DepositionOct 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prophenoloxidase activating proteinase-2


Theoretical massNumber of molelcules
Total (without water)5,7901
Polymers5,7901
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Prophenoloxidase activating proteinase-2


Mass: 5789.503 Da / Num. of mol.: 1 / Fragment: second Clip domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Gene: PAP-2 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q2FAY5, UniProt: Q8I917*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1 mM Dual-Clip domain U-15N,13C, 100 mM phosphate buffer NA, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 8.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBrukercollection
Sparkydata analysis
NMRPipeprocessing
CNSstructure solution
CNSrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 753 restraints, 690 are NOE-derived distance constraints, 27 dihedral angle restraints, 36 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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