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- PDB-1zfl: Solution structure of III-A, the major intermediate in the oxidat... -

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Basic information

Entry
Database: PDB / ID: 1zfl
TitleSolution structure of III-A, the major intermediate in the oxidative folding of leech carboxypeptidase inhibitor
ComponentsMetallocarboxypeptidase inhibitor
KeywordsHYDROLASE INHIBITOR / carboxypeptidase inhibitor / folding intermediate / oxidative folding / four-stranded antiparallel beta-sheet
Function / homologyCarboxypeptidase inhibitor / Proteinase inhibitor I46, leech metallocarboxypeptidase inhibitor / Carboxypeptidase Inhibitor; Chain A / metalloendopeptidase inhibitor activity / 2-Layer Sandwich / Alpha Beta / Metallocarboxypeptidase inhibitor
Function and homology information
Biological speciesHirudo medicinalis (medicinal leech)
MethodSOLUTION NMR / simulated annealing
AuthorsArolas, J.L. / D'Silva, L. / Popowicz, G.M. / Aviles, F.X. / Holak, T.A. / Ventura, S.
Citation
Journal: STRUCTURE / Year: 2005
Title: NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor
Authors: Arolas, J.L. / D'Silva, L. / Popowicz, G.M. / Aviles, F.X. / Holak, T.A. / Ventura, S.
#1: Journal: NAT.STRUCT.MOL.BIOL. / Year: 2000
Title: Structure of a novel leech carboxypeptidase inhibitor determined free in solution and in complex with human carboxypeptidase A2
Authors: Reverter, D. / Fernandez-Catalan, C. / Baumgartner, R. / Pfander, R. / Huber, R. / Bode, W. / Vendrell, J. / Holak, T.A. / Aviles, F.X.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Role of kinetic intermediates in the folding of leech carboxypeptidase inhibitor
Authors: Arolas, J.L. / Bronsoms, S. / Lorenzo, J. / Aviles, F.X. / Chang, J.Y. / Ventura, S.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallocarboxypeptidase inhibitor


Theoretical massNumber of molelcules
Total (without water)7,3971
Polymers7,3971
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 / 40structures with the lowest energy
RepresentativeModel #20closest to the average

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Components

#1: Protein Metallocarboxypeptidase inhibitor / Leech carboxypeptidase inhibitor / LCI / inhibitor of A/B metallocarboxypeptidases


Mass: 7397.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The III-A intermediate, containing three native disulfide bonds, has been directly isolated from the oxidative folding reaction of the leech carboxypeptidase inhibitor (LCI; four disulfide bonds)
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P81511

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
1411H-15N HSQC
1521H-15N HSQC
NMR detailsText: amide proton exchange experiments were carried out

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 15N-labeled III-A intermediate; 90% H2O, 10% D2O90% H2O/10% D2O
21mM 15N-labeled III-A intermediate; 100% D2O100% D2O
Sample conditionsIonic strength: 20mM phosphate buffer / pH: 3.5 / Pressure: ambient / Temperature: 300 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 software
NameVersionDeveloperClassification
XwinNMRBruker softwarecollection
SparkySPARKY 3Goddard and Knellerprocessing
SparkySPARKY 3Goddard and Knellerdata analysis
CNSBrungerstructure solution
CNSBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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