[English] 日本語
Yorodumi
- PDB-6u2a: ShyA endopeptidase from Vibrio cholera (open form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u2a
TitleShyA endopeptidase from Vibrio cholera (open form)
ComponentsShyA endopeptidase
KeywordsHYDROLASE / M23 peptidase / peptidoglycan / crosslinks / periplasm
Function / homology
Function and homology information


lysostaphin / septum digestion after cytokinesis / peptidoglycan binding / metalloendopeptidase activity / hydrolase activity / metal ion binding / plasma membrane
Similarity search - Function
Opacity-associated protein A / Opacity-associated protein A LysM-like domain / Csd3-like, second N-terminal domain / Csd3 second domain / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif
Similarity search - Domain/homology
Cell wall endopeptidase family M23/M37 / Cell wall endopeptidase, family M23/M37
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSaper, M.A. / Kelley, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis of peptidoglycan endopeptidase regulation.
Authors: Shin, J.H. / Sulpizio, A.G. / Kelley, A. / Alvarez, L. / Murphy, S.G. / Fan, L. / Cava, F. / Mao, Y. / Saper, M.A. / Dorr, T.
History
DepositionAug 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ShyA endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6902
Polymers45,6251
Non-polymers651
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.272, 82.492, 82.522
Angle α, β, γ (deg.)90.000, 102.692, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

-
Components

#1: Protein ShyA endopeptidase


Mass: 45624.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ShyA / Plasmid: pET28-VcShyA-His6
Details (production host): Full-length ShyA followed by His6
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2(DE3)
References: UniProt: A0A0H6MKE7, UniProt: Q9KN86*PLUS, lysostaphin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 59.9 % / Description: elongated prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein (0.5 microliter): 18 mg/ml in 20 mM Tris-HCl, 150 mM NaCl pH 7.6 Precipitant (0.5 microliter): 0.25 M sodium citrate, 10% polyethylene glycol 3350, 0.1 M Tris-HCl pH 6.0
PH range: 6-7.5

-
Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07811 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07811 Å / Relative weight: 1
ReflectionResolution: 2.025→54.9 Å / Num. obs: 17391 / % possible obs: 54.1 % / Redundancy: 7 % / Biso Wilson estimate: 60.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.011 / Rrim(I) all: 0.059 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.026-2.2766.21.131.68700.5490.4871.23466.7
6.143-54.8496.40.04119.48690.9960.0170.04573.3

-
Processing

Software
NameVersionClassification
PHENIXdev_3580refinement
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
STARANISO1.0.5data scaling
autoPROC1.0.5data scaling
XDSJan 26, 2018data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GUI

2gui


Resolution: 2.3→36.58 Å / SU ML: 0.2891 / Cross valid method: FREE R-VALUE / Phase error: 38.328
RfactorNum. reflection% reflectionSelection details
Rfree0.2936 842 5.15 %Random
Rwork0.2538 ---
obs-16347 74.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.09 Å2
Refine analyzeLuzzati d res low obs: 40 Å
Refinement stepCycle: LAST / Resolution: 2.3→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 1 10 2863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342911
X-RAY DIFFRACTIONf_angle_d0.6353929
X-RAY DIFFRACTIONf_chiral_restr0.0473424
X-RAY DIFFRACTIONf_plane_restr0.0033513
X-RAY DIFFRACTIONf_dihedral_angle_d14.7361760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.4496740.36951172X-RAY DIFFRACTION34.07
2.44-2.630.3936890.36851816X-RAY DIFFRACTION52.65
2.63-2.90.35951470.35612560X-RAY DIFFRACTION74.04
2.9-3.320.36211890.32873368X-RAY DIFFRACTION97
3.32-4.180.27381630.24763404X-RAY DIFFRACTION97.75
4.18-36.580.25641800.21073185X-RAY DIFFRACTION90.46

+
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