[English] 日本語
Yorodumi
- PDB-8qk9: Structure of E. coli LpxH in complex with JEDI-1444 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qk9
TitleStructure of E. coli LpxH in complex with JEDI-1444
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / Lipid A biosynthesis pathway Endotoxin UDP-diacyl-glucosamine lipid X Gram-negative bacteria Lipopolysaccharides
Function / homology
Function and homology information


UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / lipid A biosynthetic process / extrinsic component of plasma membrane / manganese ion binding / cytoplasm
Similarity search - Function
UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase LpxH-like / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
: / : / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSooriyaarachchi, S. / Bergfors, T. / Jones, T.A. / Mowbray, S.L.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.
Authors: Huseby, D.L. / Cao, S. / Zamaratski, E. / Sooriyaarachchi, S. / Ahmad, S. / Bergfors, T. / Krasnova, L. / Pelss, J. / Ikaunieks, M. / Loza, E. / Katkevics, M. / Bobileva, O. / Cirule, H. / ...Authors: Huseby, D.L. / Cao, S. / Zamaratski, E. / Sooriyaarachchi, S. / Ahmad, S. / Bergfors, T. / Krasnova, L. / Pelss, J. / Ikaunieks, M. / Loza, E. / Katkevics, M. / Bobileva, O. / Cirule, H. / Gukalova, B. / Grinberga, S. / Backlund, M. / Simoff, I. / Leber, A.T. / Berruga-Fernandez, T. / Antonov, D. / Konda, V.R. / Lindstrom, S. / Olanders, G. / Brandt, P. / Baranczewski, P. / Vingsbo Lundberg, C. / Liepinsh, E. / Suna, E. / Jones, T.A. / Mowbray, S.L. / Hughes, D. / Karlen, A.
History
DepositionSep 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5704
Polymers27,8631
Non-polymers7073
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-13 kcal/mol
Surface area10790 Å2
Unit cell
Length a, b, c (Å)122.309, 81.178, 32.974
Angle α, β, γ (deg.)90.00, 103.32, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein UDP-2,3-diacylglucosamine hydrolase


Mass: 27863.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lpxH / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: A0A066QL39
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VQ9 / 2-[methyl(methylsulfonyl)amino]-~{N}-[4-[4-[3-(trifluoromethyl)phenyl]piperazin-1-yl]sulfonylphenyl]benzamide


Mass: 596.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27F3N4O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.86 Å3/Da / Density % sol: 56.97 % / Description: Bypiramydal shaped crystal
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: Morpheus III - G9 1.2 % Cholic acid derivatives mix 0.1 M Buffer System 2 7.5 Precipitant Mix 1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.918401 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918401 Å / Relative weight: 1
ReflectionResolution: 1.9→67 Å / Num. obs: 24774 / % possible obs: 99.4 % / Redundancy: 7.1 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 24774 / CC1/2: 0.814

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→50.01 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.539 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21174 1293 5.2 %RANDOM
Rwork0.17771 ---
obs0.17949 23478 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.524 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å21.66 Å2
2---3.71 Å2-0 Å2
3---1.06 Å2
Refinement stepCycle: 1 / Resolution: 1.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 42 74 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161738
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6532599
X-RAY DIFFRACTIONr_angle_other_deg0.51.5724023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.22515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7410310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022169
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.363.832918
X-RAY DIFFRACTIONr_mcbond_other3.3583.832918
X-RAY DIFFRACTIONr_mcangle_it4.4675.7221144
X-RAY DIFFRACTIONr_mcangle_other4.4675.7231145
X-RAY DIFFRACTIONr_scbond_it4.1654.2851005
X-RAY DIFFRACTIONr_scbond_other4.0914.255961
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8966.2121392
X-RAY DIFFRACTIONr_long_range_B_refined7.73249.4512072
X-RAY DIFFRACTIONr_long_range_B_other7.69748.2012013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 86 -
Rwork0.268 1768 -
obs--100 %

+
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://pdbjlvh1.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