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- PDB-2lu1: pfsub2 solution NMR structure -

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Basic information

Entry
Database: PDB / ID: 2lu1
Titlepfsub2 solution NMR structure
ComponentsSubtilase
KeywordsHYDROLASE / Sub2 inhibitor prodomain
Function / homology
Function and homology information


microneme membrane / subtilisin / membrane protein ectodomain proteolysis / membrane => GO:0016020 / serine-type endopeptidase activity / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2370 / Subtilisin-like protease 2, prodomain / Prodomain subtilisin 2 / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily ...Alpha-Beta Plaits - #2370 / Subtilisin-like protease 2, prodomain / Prodomain subtilisin 2 / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-like protease 2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodSOLUTION NMR / simulated annealing
AuthorsHe, Y. / Chen, Y. / Ruan, B. / O'Brochta, D. / Bryan, P. / Orban, J.
CitationJournal: Proteins / Year: 2012
Title: Solution NMR structure of a sheddase inhibitor prodomain from the malarial parasite Plasmodium falciparum.
Authors: He, Y. / Chen, Y. / Oganesyan, N. / Ruan, B. / O'Brochta, D. / Bryan, P.N. / Orban, J.
History
DepositionJun 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilase


Theoretical massNumber of molelcules
Total (without water)17,7211
Polymers17,7211
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 / 500structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein Subtilase /


Mass: 17721.326 Da / Num. of mol.: 1 / Fragment: sheddase inhibitor prodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: sub-2 / Plasmid: pPal7 / Production host: Escherichia coli (E. coli) / References: UniProt: O97364

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D H(CCO)NH

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Sample preparation

DetailsContents: 0.3 - 0.4 mM [U-13C; U-15N] pfsub2, 100 mM potassium phosphate, 10 mM sodium azide, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMpfsub2-1[U-13C; U-15N]0.3-0.41
100 mMpotassium phosphate-21
10 mMsodium azide-31
5 %D2O-41
Sample conditionsIonic strength: 0.1 / pH: 7.0 / Pressure: ambient / Temperature: 310 K

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NMR measurement

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

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Processing

NMR softwareName: CNS / Version: 1.21 / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 956 / NOE intraresidue total count: 601 / NOE long range total count: 88 / NOE medium range total count: 56 / NOE sequential total count: 211
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 500 / Conformers submitted total number: 20

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