[English] 日本語
Yorodumi
- PDB-5kvp: Solution structure of the catalytic domain of zoocin A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kvp
TitleSolution structure of the catalytic domain of zoocin A
ComponentsZoocin A endopeptidase
KeywordsHYDROLASE / exoenzyme / anti-microbial / endopeptidase
Function / homology
Function and homology information


lysostaphin / carbohydrate transport / hydrolase activity
Similarity search - Function
Lytic exoenzyme, target recognition domain / Lytic exoenzyme, target recognition domain superfamily / Target recognition domain of lytic exoenzyme / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / Peptidase, M23/M37 family
Similarity search - Component
Biological speciesStreptococcus equi subsp. zooepidemicus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTimkovich, R. / Xing, M. / Simmonds, R.S.
CitationJournal: Proteins / Year: 2017
Title: Solution structure of the Cys74 to Ala74 mutant of the recombinant catalytic domain of Zoocin A.
Authors: Xing, M. / Simmonds, R.S. / Timkovich, R.
History
DepositionJul 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jul 26, 2017Group: Data collection / Database references / Structure summary
Category: entity / pdbx_database_related / pdbx_nmr_ensemble
Item: _entity.pdbx_number_of_molecules / _pdbx_nmr_ensemble.conformer_selection_criteria
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zoocin A endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9193
Polymers16,8541
Non-polymers652
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1

-
Components

#1: Protein Zoocin A endopeptidase


Mass: 16853.678 Da / Num. of mol.: 1 / Mutation: C85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus equi subsp. zooepidemicus (bacteria)
Gene: zooA / Production host: Escherichia coli (E. coli) / References: UniProt: O54308
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
Nonpolymer detailsThe oxygen atom in UNL ligand comes from water or phosphate ions in the buffer

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
151isotropic13D HN(CO)CA
1251isotropic13D HN(CA)CO
161isotropic13D (H)CCH-TOCSY
171isotropic13D HNHA
181isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY
1101isotropic13D CCC-TOCSY
1111isotropic13D HCC-TOCSY
2122isotropic12D 1H-15N HSQC
2132isotropic13D HNCO
2142isotropic13D HNCA
2262isotropic13D HN(CA)CO
2152isotropic13D HN(CA)CB
2162isotropic13D HN(CO)CA
2172isotropic13D (H)CCH-TOCSY
2182isotropic13D HNHA
2192isotropic13D 1H-15N NOESY
2202isotropic13D 1H-13C NOESY
2212isotropic13D CCC-TOCSY
2222isotropic13D HCC-TOCSY
3233isotropic12D 1H-15N HSQC
3243isotropic13D 1H-15N NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM potassium phosphate, 0.1 mM sodium azide, 1.1 mM [U-95% 13C; U-90% 15N] Protein, 95% H2O/5% D2O1.1 MM [U-95% 13C; U-90% 15N] Protein95% H2O/5% D2O
solution210 mM potassium phosphate, 0.1 mM sodium azide, 0.5 mM [U-95% 13C; U-90% 15N] protein, 95% H2O/5% D2O0.5 MM [U-95% 13C; U-90% 15N] Protein95% H2O/5% D2O
solution310 mM potassium phosphate, 0.1 mM sodium azide, 1.0 mM [U-90% 15N] protein, 95% H2O/5% D2O15N_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMpotassium phosphatenatural abundance1
0.1 mMsodium azidenatural abundance1
1.1 mMProtein[U-95% 13C; U-90% 15N]1
10 mMpotassium phosphatenatural abundance2
0.1 mMsodium azidenatural abundance2
0.5 mMprotein[U-95% 13C; U-90% 15N]2
10 mMpotassium phosphatenatural abundance3
0.1 mMsodium azidenatural abundance3
1.0 mMprotein[U-90% 15N]3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.02 M1.1 MM [U-95% 13C; U-90% 15N] Protein_condition5.6 1.0 atm297 K
20.02 M0.5 MM [U-95% 13C; U-90% 15N] Protein_condition5.6 1 atm297 K
30.02 M15N_sample_condition5.6 1 atm297 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.3BRUNGER, ADAMS, CLORE, GROS, NILGES AND READrefinement
CNS1.3structure solution
NMRViewstructure solution
NMRPipestructure solution
NMRDrawstructure solution
TALOS+structure solution
TopSpin1.2structure solution
DEEPVIEW/SWISS-PDB VIEWERstructure solution
PROCHECKNMRstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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