[English] 日本語
Yorodumi
- PDB-6i4a: Structure of P. aeruginosa LpxC with compound 18d: (2R)-N-Hydroxy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i4a
TitleStructure of P. aeruginosa LpxC with compound 18d: (2R)-N-Hydroxy-4-(6-((1-(hydroxymethyl)cyclopropyl)buta-1,3-diyn-1-yl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)-yl)-2-methyl-2-(methylsulfonyl)butanamide
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
KeywordsHYDROLASE / Inhibitor
Function / homology
Function and homology information


: / UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-H2Q / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa LESB58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsSurivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. ...Surivet, J.-P. / Panchaud, P. / Specklin, J.-L. / Diethelm, S. / Blumstein, A.-C. / Gauvin, J.-C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Enderlin-Paput, M. / Lange, R. / Bur, D. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Hermann, C. / Locher, H.H. / Seiler, P. / Mac Sweeney, A. / Hubschwerlen, C. / Ritz, D. / Rueedi, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria.
Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. ...Authors: Surivet, J.P. / Panchaud, P. / Specklin, J.L. / Diethelm, S. / Blumstein, A.C. / Gauvin, J.C. / Jacob, L. / Masse, F. / Mathieu, G. / Mirre, A. / Schmitt, C. / Lange, R. / Tidten-Luksch, N. / Gnerre, C. / Seeland, S. / Herrmann, C. / Seiler, P. / Enderlin-Paput, M. / Mac Sweeney, A. / Wicki, M. / Hubschwerlen, C. / Ritz, D. / Rueedi, G.
History
DepositionNov 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6463
Polymers33,1471
Non-polymers4992
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.071, 66.485, 63.193
Angle α, β, γ (deg.)90.000, 90.648, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-acyl-GlcNAc deacetylase / UDP-3-O-[R-3-hydroxymyristoyl]-N-acetylglucosamine deacetylase


Mass: 33146.617 Da / Num. of mol.: 1 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa LESB58 (bacteria)
Gene: lpxC, PLES_47851 / Production host: Escherichia coli (E. coli)
References: UniProt: B7UZI4, UDP-3-O-acyl-N-acetylglucosamine deacetylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-H2Q / (2~{R})-4-[6-[4-[1-(hydroxymethyl)cyclopropyl]buta-1,3-diynyl]-3-oxidanylidene-1~{H}-pyrrolo[1,2-c]imidazol-2-yl]-2-methyl-2-methylsulfonyl-~{N}-oxidanyl-butanamide


Mass: 433.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris pH 8.5, 20 % PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→36.003 Å / Num. obs: 14233 / % possible obs: 99.7 % / Redundancy: 3.45 % / CC1/2: 0.993 / Net I/σ(I): 4.8
Reflection shellResolution: 2.25→2.39 Å / Mean I/σ(I) obs: 1.2 / CC1/2: 0.46 / Rrim(I) all: 1.25 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238 2018/15/10refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ves

2ves


Resolution: 2.251→36.003 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.876 / SU B: 12.012 / SU ML: 0.273 / Cross valid method: FREE R-VALUE / ESU R: 0.426 / ESU R Free: 0.276
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2812 709 -
Rwork0.225 --
all0.228 --
obs-14226 99.587 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.019 Å20 Å2-0.473 Å2
2---1.512 Å20 Å2
3---1.541 Å2
Refinement stepCycle: LAST / Resolution: 2.251→36.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 31 71 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132457
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172311
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.6713342
X-RAY DIFFRACTIONr_angle_other_deg1.3031.6025333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.6775.222316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15221.967122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57115402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5511517
X-RAY DIFFRACTIONr_chiral_restr0.0580.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
X-RAY DIFFRACTIONr_nbd_refined0.1750.2424
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.22106
X-RAY DIFFRACTIONr_nbtor_refined0.150.21142
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2110
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.26
X-RAY DIFFRACTIONr_nbd_other0.1730.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.212
X-RAY DIFFRACTIONr_mcbond_it1.1332.9011218
X-RAY DIFFRACTIONr_mcbond_other1.1332.91217
X-RAY DIFFRACTIONr_mcangle_it1.9734.3391532
X-RAY DIFFRACTIONr_mcangle_other1.9734.3391533
X-RAY DIFFRACTIONr_scbond_it1.0723.0641239
X-RAY DIFFRACTIONr_scbond_other1.0713.0641239
X-RAY DIFFRACTIONr_scangle_it1.8574.5391803
X-RAY DIFFRACTIONr_scangle_other1.8564.541804
X-RAY DIFFRACTIONr_lrange_it3.66133.3332583
X-RAY DIFFRACTIONr_lrange_other3.59433.342568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.251-2.3090.445520.358971104098.36540.355
2.309-2.3720.361510.333984103799.80710.334
2.372-2.440.302500.394699899.79960.298
2.44-2.5150.371480.31390695699.79080.309
2.515-2.5970.315460.27889193999.7870.271
2.597-2.6880.307450.2783688399.77350.262
2.688-2.7890.309440.23184689499.55260.221
2.789-2.9020.28420.23779183499.88010.222
2.902-3.030.337400.23577081299.75370.221
3.03-3.1770.255390.22672776799.86960.21
3.177-3.3470.276360.20569573299.86340.19
3.347-3.5480.252350.21665569299.7110.199
3.548-3.790.252330.19762566199.54610.182
3.79-4.090.267300.1775826121000.163
4.09-4.4750.204290.1625465751000.149
4.475-4.9940.276240.174684921000.161
4.994-5.7480.24240.19844747399.57720.18
5.748-6.9950.286190.19636338399.73890.179
6.995-9.7110.181150.17329431099.67740.16
9.711-36.0030.2770.217418896.27660.198

+
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