[English] 日本語
Yorodumi
- PDB-1zfl: Solution structure of III-A, the major intermediate in the oxidat... -

+
Open data


ID or keywords:

Loading...

-
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 / peptidase 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metallocarboxypeptidase inhibitor


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

-
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
Has protein modificationY

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more