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- PDB-2l4v: Three Dimensional Structure of Pineapple Cystatin -

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Basic information

Entry
Database: PDB / ID: 2l4v
TitleThree Dimensional Structure of Pineapple Cystatin
ComponentsCystatin
KeywordsHYDROLASE INHIBITOR / Cystatin / protease inhibitor
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity
Similarity search - Function
Cystatin-related, plant / Aspartic acid proteinase inhibitor / Cystatin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Cysteine proteinase inhibitor / Cysteine proteinase inhibitor
Similarity search - Component
Biological speciesAnanas comosus (pineapple)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsChyan, C.C.L. / Deli, I.I. / Chen, B.B.J.
Citation
Journal: Biomol.Nmr Assign. / Year: 2012
Title: Resonance assignments and secondary structure of a phytocystatin from Ananas comosus
Authors: Irene, D. / Chen, B.J. / Lo, S.H. / Liu, T.H. / Tzen, J.T.C. / Chyan, C.L.
#1: Journal: Plos One / Year: 2012
Title: Solution structure of a phytocystatin from Ananas comosus and its molecular interaction with papain
Authors: Irene, D. / Chung, T.Y. / Chen, B.J. / Liu, T.H. / Li, F.Y. / Tzen, J.T.C. / Wang, C.I. / Chyan, C.L.
History
DepositionOct 15, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystatin


Theoretical massNumber of molelcules
Total (without water)15,4721
Polymers15,4721
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Cystatin /


Mass: 15472.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ananas comosus (pineapple) / Production host: Escherichia coli (E. coli) / References: UniProt: Q687J0, UniProt: C9W181*PLUS

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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-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D HNCO
1613D HN(CA)CO
1713D CBCA(CO)NH
1813D HN(CA)CB
1913D C(CO)NH
11013D HBHA(CO)NH
11113D H(CCO)NH
11212D DQF-COSY
11312D 1H-1H NOESY
11413D (H)CCH-COSY
11513D (H)CCH-TOCSY
11613D 1H-15N TOCSY
11713D 1H-15N NOESY
11813D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 to 1 mM [U-99% 13C; U-99% 15N] Pineapple Cystatin-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: Pineapple Cystatin-1 / Isotopic labeling: [U-99% 13C; U-99% 15N] / Conc. range: 0.5-1
Sample conditionsIonic strength: 0.02 / pH: 6.5 / Pressure: ambient / Temperature: 303 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 software
NameVersionDeveloperClassification
AURELIA3.9.7Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerdata analysis
AURELIA3.9.7Neidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichcalculation;
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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