[English] 日本語
Yorodumi
- PDB-5u86: Structure of the Aquifex aeolicus LpxC/LPC-069 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u86
TitleStructure of the Aquifex aeolicus LpxC/LPC-069 complex
ComponentsUDP-3-O-acyl-N-acetylglucosamine deacetylase
Keywordshydrolase/hydrolase inhibitor / LpxC lipid A antibiotic LPS / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / 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 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-81V / PHOSPHATE ION / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsNajeeb, J. / Lee, C.-J. / Zhou, P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI094475 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115355 United States
CitationJournal: MBio / Year: 2017
Title: Curative Treatment of Severe Gram-Negative Bacterial Infections by a New Class of Antibiotics Targeting LpxC.
Authors: Lemaitre, N. / Liang, X. / Najeeb, J. / Lee, C.J. / Titecat, M. / Leteurtre, E. / Simonet, M. / Toone, E.J. / Zhou, P. / Sebbane, F.
History
DepositionDec 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: 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
A: UDP-3-O-acyl-N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4189
Polymers31,4531
Non-polymers9658
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.990, 65.990, 132.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 1 molecules A

#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: 31453.012 Da / Num. of mol.: 1 / Mutation: C181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: lpxC, envA, aq_1772 / Production host: Escherichia coli (E. coli)
References: UniProt: O67648, UDP-3-O-acyl-N-acetylglucosamine deacetylase

-
Non-polymers , 6 types, 449 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-81V / N-[(2S,3S)-4,4-difluoro-3-hydroxy-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-({4-[(morpholin-4-yl)methyl]phenyl}ethynyl)benzamide


Mass: 487.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27F2N3O5
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.25 mg/mL compound, 4 mg/mL protein, 50 mM potassium chloride, 12.5 mM HEPES pH 7.0, 1 mM dithiothreitol, 25 microM zinc sulfate, 0.5% DMSO, 1.25 M diammonium hydrogen phosphate, 0.05 M ...Details: 0.25 mg/mL compound, 4 mg/mL protein, 50 mM potassium chloride, 12.5 mM HEPES pH 7.0, 1 mM dithiothreitol, 25 microM zinc sulfate, 0.5% DMSO, 1.25 M diammonium hydrogen phosphate, 0.05 M Tris pH 7.7, 2.5% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→29.531 Å / Num. obs: 41386 / % possible obs: 99.99 % / Redundancy: 12.4 % / Net I/σ(I): 20.13

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DRO

5dro


Resolution: 1.62→29.531 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 15.08
RfactorNum. reflection% reflection
Rfree0.1537 2009 4.86 %
Rwork0.1388 --
obs0.1396 41379 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→29.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 59 441 2656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062485
X-RAY DIFFRACTIONf_angle_d0.8993371
X-RAY DIFFRACTIONf_dihedral_angle_d10.1061504
X-RAY DIFFRACTIONf_chiral_restr0.062363
X-RAY DIFFRACTIONf_plane_restr0.009433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6199-1.66050.21121420.16752814X-RAY DIFFRACTION100
1.6605-1.70530.20351430.16242793X-RAY DIFFRACTION100
1.7053-1.75550.17261420.15162793X-RAY DIFFRACTION100
1.7555-1.81220.17311440.15432819X-RAY DIFFRACTION100
1.8122-1.87690.18491400.15062833X-RAY DIFFRACTION100
1.8769-1.95210.17541440.14922785X-RAY DIFFRACTION100
1.9521-2.04090.16841430.14482792X-RAY DIFFRACTION100
2.0409-2.14850.17691470.1382826X-RAY DIFFRACTION100
2.1485-2.2830.15571420.13732824X-RAY DIFFRACTION100
2.283-2.45920.14731440.13942810X-RAY DIFFRACTION100
2.4592-2.70660.14671440.14062792X-RAY DIFFRACTION100
2.7066-3.09780.17221430.14732814X-RAY DIFFRACTION100
3.0978-3.90150.11381450.12472843X-RAY DIFFRACTION100
3.9015-29.53610.13431460.12382832X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.24810.09132.25650.93350.24951.2707-0.1294-0.20020.50770.0549-0.03550.0146-0.07-0.0560.16090.0918-0.00760.0070.10050.00170.0848-26.912830.6512-16.911
21.93890.103-0.06971.2327-0.20271.39470.00860.13930.1473-0.095-0.0505-0.0709-0.02690.10460.04190.06220.0017-0.00290.06640.01420.0746-25.186625.7023-24.7554
32.4353-0.9260.31082.0994-0.29050.05750.0199-0.059-0.0168-0.0397-0.08880.145-0.0236-0.17840.07690.0671-0.0230.02770.08260.02520.0625-38.097919.7068-20.6872
41.633-0.25511.34961.50080.17873.4320.11440.1546-0.2306-0.0694-0.0253-0.05220.36270.3138-0.0610.15590.02390.01540.0973-0.00190.1338-23.91612.2308-18.8572
53.99970.7973-0.44621.5866-0.33411.2955-0.0228-0.19-0.20790.0062-0.0156-0.05580.07950.09650.04860.11380.01670.00120.0611-0.00040.0543-16.197713.9176-11.6346
62.19691.0186-1.00611.904-0.76852.37930.0757-0.2111-0.1170.1535-0.097-0.04940.08710.2212-0.00980.08140.0167-0.01580.09760.00740.0787-14.00214.726-5.0627
71.28310.37680.62271.6486-0.08862.67160.03480.0045-0.1118-0.0491-0.03640.00270.14470.03130.00740.07470.01570.00870.04690.00090.0677-26.771610.2381-20.5173
86.02511.28113.32663.35110.82186.5671-0.00820.64010.0272-0.5260.02650.05940.0559-0.1011-0.01290.21010.03060.02990.1626-0.00130.0879-25.769910.3389-33.4151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 191 )
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 221 )
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 252 )
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 270 )

+
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