[English] 日本語
Yorodumi
- PDB-7a10: LppS with covalent adduct derived from 1g -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a10
TitleLppS with covalent adduct derived from 1g
ComponentsL,D-transpeptidase 2
KeywordsLIGASE / Transpeptidase / cell wall / peptidoglycan / antibiotic / Beta-lactam / Covalent inhibitor / Mycobacterium tuberculosis
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / metal ion binding / plasma membrane
Similarity search - Function
Bacterial Ig domain, transpeptidase-associated / Bacterial Ig domain / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
4-methoxycyclohexa-2,5-diene-1-thione / L,D-transpeptidase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchnell, R. / Steiner, E.M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vinnova Sweden
CitationJournal: Cell Chem Biol / Year: 2021
Title: N-Thio-beta-lactams targeting L,D-transpeptidase-2, with activity against drug-resistant strains of Mycobacterium tuberculosis.
Authors: Martelli, G. / Pessatti, T.B. / Steiner, E.M. / Cirillo, M. / Caso, C. / Bisognin, F. / Landreh, M. / Monte, P.D. / Giacomini, D. / Schnell, R.
History
DepositionAug 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L,D-transpeptidase 2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3024
Polymers57,0172
Non-polymers2842
Water8,323462
1
A: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6512
Polymers28,5091
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L,D-transpeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6512
Polymers28,5091
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.230, 89.806, 67.005
Angle α, β, γ (deg.)90.000, 103.960, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein L,D-transpeptidase 2 / LDT 2 / Ldt(Mt2)


Mass: 28508.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct used here contains two domains: domain-B (Ig-like) and domain-C (catalytic transpeptidase domain), residue range 149-408 of the full length protein.
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pNIC28-Bsa4
Details (production host): N-terminal His6-tag, removable by TEV cleavage
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases
#2: Chemical ChemComp-QU5 / 4-methoxycyclohexa-2,5-diene-1-thione


Mass: 142.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.5 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: Well solution: 0.1 M Na-Citrate pH 4.25 / 17.5% PEG 6K The crystals were cryo-protected by dipping them in mother liquor with increased 25% PEG 6K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.82656 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2019 / Details: mirrors (VFM, HFM)
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.85→39.44 Å / Num. obs: 42829 / % possible obs: 96.5 % / Observed criterion σ(I): 1.2 / Redundancy: 6.5 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.099 / Net I/σ(I): 11.7
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2066 / CC1/2: 0.548 / Rpim(I) all: 0.847 / % possible all: 75.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LBG

5lbg


Resolution: 1.85→39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.044 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2110 4.9 %RANDOM
Rwork0.1869 ---
obs0.1887 40691 96.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.93 Å2 / Biso mean: 33.308 Å2 / Biso min: 16.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0 Å20.01 Å2
2--1.24 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 1.85→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 18 463 4457
Biso mean--42.61 39.58 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194131
X-RAY DIFFRACTIONr_bond_other_d0.0020.023735
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.9165648
X-RAY DIFFRACTIONr_angle_other_deg1.0583.0028573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.78624.398191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15315594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0711520
X-RAY DIFFRACTIONr_chiral_restr0.1160.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214797
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02983
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 111 -
Rwork0.309 2386 -
all-2497 -
obs--75.97 %

+
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