[English] 日本語
Yorodumi
- PDB-8aik: Crystal structure of DltE from L. plantarum, tartare bound form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8aik
TitleCrystal structure of DltE from L. plantarum, tartare bound form
ComponentsBeta-lactamase family protein
KeywordsCELL CYCLE / carboxyesterase / D-alanylation / lipoteichoic acids
Function / homologyserine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / membrane / L(+)-TARTARIC ACID / Beta-lactamase class C and other penicillinbinding protein
Function and homology information
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRavaud, S. / Nikolopoulos, N. / Grangeasse, C.
Funding support France, 2items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
Agence Nationale de la Recherche (ANR)18-CE15-0011 France
CitationJournal: Elife / Year: 2023
Title: Structure-function analysis of Lactiplantibacillus plantarum DltE& reveals D-alanylated lipoteichoic acids as direct cues supporting Drosophila juvenile growth.
Authors: Nikolopoulos, N. / Matos, R. / Ravaud, S. / Courtin, P. / Akherraz, H. / Palussiere, S. / Gueguen-Chaignon, V. / Salomon-Mallet, M. / Guillot, A. / Guerardel, Y. / Chapot-Chartier, M.P. / ...Authors: Nikolopoulos, N. / Matos, R. / Ravaud, S. / Courtin, P. / Akherraz, H. / Palussiere, S. / Gueguen-Chaignon, V. / Salomon-Mallet, M. / Guillot, A. / Guerardel, Y. / Chapot-Chartier, M.P. / Grangeasse, C. / Leulier, F.
History
DepositionJul 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 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: Beta-lactamase family protein
B: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0955
Polymers83,6452
Non-polymers4503
Water10,305572
1
A: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9732
Polymers41,8231
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1233
Polymers41,8231
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.690, 103.730, 152.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-lactamase family protein / Class A beta-lactamase-related serine hydrolase / Penicillin-binding protein PbpX / Serine-type D- ...Class A beta-lactamase-related serine hydrolase / Penicillin-binding protein PbpX / Serine-type D-Ala-D-Ala carboxypeptidase


Mass: 41822.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria)
Gene: pbpX2, pbpX_4, C7M36_02596, E3O64_07015, E3U93_06380, FEE41_04205, IV39_GL001648, LPJSA22_01868, SN35N_2987
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P7JVD2, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium tartrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.95→46.384 Å / Num. obs: 56946 / % possible obs: 99.5 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3918 / CC1/2: 0.787

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AGR

8agr


Resolution: 1.95→46.384 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.061 / SU ML: 0.112 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2211 2810 4.941 %
Rwork0.1825 54061 -
all0.184 --
obs-56871 99.338 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.377 Å2
Baniso -1Baniso -2Baniso -3
1-0.011 Å20 Å20 Å2
2---0.001 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 30 572 5608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0115185
X-RAY DIFFRACTIONr_bond_other_d0.0360.0164719
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.6427004
X-RAY DIFFRACTIONr_angle_other_deg0.8691.55511013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.3371022
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22710917
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.93510233
X-RAY DIFFRACTIONr_chiral_restr0.0670.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021028
X-RAY DIFFRACTIONr_nbd_refined0.2180.2921
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.23886
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22507
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2430
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.27
X-RAY DIFFRACTIONr_nbd_other0.1880.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.26
X-RAY DIFFRACTIONr_mcbond_it2.533.1512582
X-RAY DIFFRACTIONr_mcbond_other2.5293.1512582
X-RAY DIFFRACTIONr_mcangle_it3.2994.7113228
X-RAY DIFFRACTIONr_mcangle_other3.2994.7123229
X-RAY DIFFRACTIONr_scbond_it3.7913.6182603
X-RAY DIFFRACTIONr_scbond_other3.7873.6172602
X-RAY DIFFRACTIONr_scangle_it5.7165.2483768
X-RAY DIFFRACTIONr_scangle_other5.7155.2483768
X-RAY DIFFRACTIONr_lrange_it7.01241.0235887
X-RAY DIFFRACTIONr_lrange_other7.01141.0345888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3452200.3163892X-RAY DIFFRACTION99.709
2.001-2.0550.3252020.2583837X-RAY DIFFRACTION99.7038
2.055-2.1150.2951790.2313819X-RAY DIFFRACTION99.8003
2.115-2.180.2562150.2143577X-RAY DIFFRACTION99.7632
2.18-2.2510.2861760.2023545X-RAY DIFFRACTION99.7855
2.251-2.330.2461940.1943433X-RAY DIFFRACTION99.8623
2.33-2.4180.261580.1813333X-RAY DIFFRACTION99.7999
2.418-2.5160.2571710.1813161X-RAY DIFFRACTION99.671
2.516-2.6270.2581360.1753098X-RAY DIFFRACTION99.5996
2.627-2.7550.2321420.1792937X-RAY DIFFRACTION99.6763
2.755-2.9040.2591410.1892720X-RAY DIFFRACTION96.5901
2.904-3.0790.2281250.192546X-RAY DIFFRACTION94.9858
3.079-3.2910.2031430.1842481X-RAY DIFFRACTION99.8858
3.291-3.5530.2151070.1992367X-RAY DIFFRACTION99.8386
3.553-3.890.1841080.1742159X-RAY DIFFRACTION99.7799
3.89-4.3450.166980.1391990X-RAY DIFFRACTION99.8565
4.345-5.010.188960.1351757X-RAY DIFFRACTION99.9461
5.01-6.1180.1841000.1651499X-RAY DIFFRACTION100
6.118-8.5780.194590.1781189X-RAY DIFFRACTION99.84

+
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