[English] 日本語
Yorodumi
- PDB-8wt4: Crystal structure of DL-endopeptidase CwlO complexed with IseA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wt4
TitleCrystal structure of DL-endopeptidase CwlO complexed with IseA
Components
  • Peptidoglycan DL-endopeptidase CwlO
  • Uncharacterized protein YoeB
KeywordsHYDROLASE / Peptidoglycan DL-endopeptidase / autolysin / a complex of DL-endopeptidase and inhibitory protein
Function / homology
Function and homology information


peptidoglycan metabolic process / Hydrolases; Acting on peptide bonds (peptidases) / cysteine-type peptidase activity / cell wall organization / endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Peptidoglycan hydrolase PcsB, coiled-coil domain / DL-endopeptidase inhibitor IseA / : / IseA DL-endopeptidase inhibitor / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Uncharacterized protein YoeB / Peptidoglycan DL-endopeptidase CwlO
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsTandukar, S. / Kwon, E. / Kim, D.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Structural analysis of the peptidoglycan DL-endopeptidase CwlO complexed with its inhibitory protein IseA.
Authors: Tandukar, S. / Kwon, E. / Kim, D.Y.
History
DepositionOct 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein YoeB
B: Peptidoglycan DL-endopeptidase CwlO


Theoretical massNumber of molelcules
Total (without water)34,3452
Polymers34,3452
Non-polymers00
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-11 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.200, 58.840, 69.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Uncharacterized protein YoeB


Mass: 20168.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yoeB, BSU18380 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O34841
#2: Protein Peptidoglycan DL-endopeptidase CwlO / D-gamma-glutamyl-meso-diaminopimelyl DL-endopeptidase / PSPA2


Mass: 14176.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: cwlO, yvcE, yzkA, BSU34800 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P40767, Hydrolases; Acting on peptide bonds (peptidases)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 30% (v/v) isopropanol, 15% (v/v) PEG 3350, 0.2 M ammonium citrate/citric acid pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.62→92.2 Å / Num. obs: 47169 / % possible obs: 96.9 % / Redundancy: 4.22 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.046 / Rrim(I) all: 0.096 / Net I/σ(I): 10
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 4.25 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2375 / Rpim(I) all: 0.41 / Rrim(I) all: 0.826 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX1.19refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→55.44 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 2330 4.96 %
Rwork0.1812 --
obs0.1825 46981 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.92 Å2
Refinement stepCycle: LAST / Resolution: 1.62→55.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 0 589 2805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042264
X-RAY DIFFRACTIONf_angle_d0.6853058
X-RAY DIFFRACTIONf_dihedral_angle_d5.678309
X-RAY DIFFRACTIONf_chiral_restr0.051335
X-RAY DIFFRACTIONf_plane_restr0.006390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.29241520.2852654X-RAY DIFFRACTION99
1.65-1.690.27811420.25162676X-RAY DIFFRACTION99
1.69-1.730.25271260.22922651X-RAY DIFFRACTION98
1.73-1.770.251190.22362636X-RAY DIFFRACTION97
1.77-1.820.26311260.21232501X-RAY DIFFRACTION93
1.82-1.870.24971450.20482621X-RAY DIFFRACTION98
1.87-1.930.33971320.2752665X-RAY DIFFRACTION98
1.93-20.241230.20892676X-RAY DIFFRACTION99
2-2.080.19131200.17162677X-RAY DIFFRACTION98
2.08-2.170.19651180.1732551X-RAY DIFFRACTION93
2.17-2.290.24161460.21032535X-RAY DIFFRACTION94
2.29-2.430.19281440.17152669X-RAY DIFFRACTION98
2.43-2.620.19911610.17182657X-RAY DIFFRACTION98
2.62-2.880.19441190.16952531X-RAY DIFFRACTION91
2.88-3.30.18081730.16112649X-RAY DIFFRACTION97
3.3-4.160.17271360.152593X-RAY DIFFRACTION93
4.16-55.440.18171480.15262709X-RAY DIFFRACTION92

+
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