[English] 日本語
Yorodumi
- PDB-2qia: Structural basis for the acyl chain selectivity and mechanism of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qia
TitleStructural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine Acyltransferase
ComponentsUDP-N-acetylglucosamine acyltransferase
KeywordsTRANSFERASE / left-handed parallel beta helix
Function / homology
Function and homology information


acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase / acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity / lipid A biosynthetic process / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 ...Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Udp N-acetylglucosamine O-acyltransferase, C-terminal domain / UDP N-acetylglucosamine O-acyltransferase, C-terminal / UDP-N-acetylglucosamine O-acyltransferase, C-terminal domain superfamily / Udp N-acetylglucosamine O-acyltransferase; Domain 2 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-U20 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsWilliams, A.H. / Raetz, C.R.H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase
Authors: Williams, A.H. / Raetz, C.R.H.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9512
Polymers28,1171
Non-polymers8341
Water7,422412
1
A: UDP-N-acetylglucosamine acyltransferase
hetero molecules

A: UDP-N-acetylglucosamine acyltransferase
hetero molecules

A: UDP-N-acetylglucosamine acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8526
Polymers84,3513
Non-polymers2,5013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area28796 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.143, 97.143, 97.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1057-

HOH

21A-1072-

HOH

31A-1255-

HOH

DetailsThe biological assembly is a homotrimer

-
Components

#1: Protein UDP-N-acetylglucosamine acyltransferase / E.C.2.3.1.129 / Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase


Mass: 28117.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: lpxa / Plasmid: pTO1 (pET 23C) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysE
References: UniProt: P0A722, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
#2: Chemical ChemComp-U20 / uridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetyl-D-glucosamine / (2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydrox ytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-4-yl (3R)-3-hydroxytetradecanoate


Mass: 833.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H53N3O19P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.8-1.4 Na/K phosphate, pH 5.6-6.3, 30%-35% Dimethyl Sulfoxide(DMSO), VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 30085 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.047 / Χ2: 3.533 / Net I/σ(I): 35.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.74-1.83.50.17828921.96893.1
1.8-1.873.50.14229732.3394.5
1.87-1.963.40.10529592.86394.9
1.96-2.063.40.08829693.49794.6
2.06-2.193.30.0729774.00695
2.19-2.363.20.06230274.30596
2.36-2.63.20.05530564.26897.3
2.6-2.983.20.04830674.41196.4
2.98-3.753.20.04230364.44394.6
3.75-503.20.03431293.50294.7

-
Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.93 Å23.56 Å
Translation1.93 Å23.56 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LXA

1lxa


Resolution: 1.74→23.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.032 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.121 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1517 5 %RANDOM
Rwork0.186 ---
obs0.188 30044 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.214 Å2
Refinement stepCycle: LAST / Resolution: 1.74→23.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 55 412 2441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222067
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9742802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33123.48389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80815326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.471515
X-RAY DIFFRACTIONr_chiral_restr0.0650.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021543
X-RAY DIFFRACTIONr_nbd_refined0.180.21103
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2316
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.246
X-RAY DIFFRACTIONr_mcbond_it0.3851.51328
X-RAY DIFFRACTIONr_mcangle_it0.58822072
X-RAY DIFFRACTIONr_scbond_it1.1153813
X-RAY DIFFRACTIONr_scangle_it1.8844.5730
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 103 -
Rwork0.271 2015 -
obs-2118 92.49 %

+
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