[English] 日本語
Yorodumi
- PDB-1lxa: UDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lxa
TitleUDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE
ComponentsUDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
KeywordsACYLTRANSFERASE / TRANSFERASE / LIPID A BIOSYNTHESIS / LIPID SYNTHESIS
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 / membrane / cytoplasm / cytosol
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 / Hexapeptide repeat proteins ...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 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRoderick, S.L.
Citation
Journal: Science / Year: 1995
Title: A left-handed parallel beta helix in the structure of UDP-N-acetylglucosamine acyltransferase.
Authors: Raetz, C.R. / Roderick, S.L.
#1: Journal: Proteins / Year: 1995
Title: Crystallization of Udp N-Acetylglucosamine O-Acyltransferase from Escherichia Coli
Authors: Pfitzner, U. / Raetz, C.R.H. / Roderick, S.L.
History
DepositionOct 7, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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 O-ACYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)28,1171
Polymers28,1171
Non-polymers00
Water00
1
A: UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE

A: UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE

A: UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)84,3513
Polymers84,3513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5150 Å2
ΔGint-39 kcal/mol
Surface area30440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.000, 99.000, 99.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein UDP N-ACETYLGLUCOSAMINE O-ACYLTRANSFERASE / LPXA


Mass: 28117.018 Da / Num. of mol.: 1 / Mutation: S64Q, V65F, D125H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: LPXA / Plasmid: PSR1 / Gene (production host): LPXA / Production host: Escherichia coli (E. coli)
References: UniProt: P0A722, acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase
Compound detailsMET 1 THROUGH ILE 186 COMPRISES THE LEFT-HANDED BETA-HELICAL DOMAIN WITH TWO LOOP EXCURSIONS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.21 %
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.8 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.9 Msodium phosphate1reservoiror potassium phosphate
215-20 %(v/v)dimethylsulfoxide1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. obs: 8868 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Num. measured all: 79727 / Rmerge(I) obs: 0.08

-
Processing

Software
NameVersionClassification
X-PLORmodel building
TNT5Erefinement
X-PLORrefinement
XDSdata reduction
X-PLORphasing
RefinementResolution: 2.6→99 Å / Isotropic thermal model: KNOWLEDGE-BASED / σ(F): 0 / Stereochemistry target values: TNT SUPPLIED
RfactorNum. reflection% reflection
Rwork0.184 --
obs-8868 87 %
Solvent computationSolvent model: TWO PARAMETER RECIPROCAL SPACE / Bsol: 250 Å2 / ksol: 0.874 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 0 1974
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONx_bond_d0.01220100.8
X-RAY DIFFRACTIONx_angle_deg2.427131.3
X-RAY DIFFRACTIONx_dihedral_angle_d26.412130
Software
*PLUS
Name: X-PLOR/TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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