[English] 日本語
Yorodumi
- PDB-5n6m: Structure of the membrane integral lipoprotein N-acyltransferase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n6m
TitleStructure of the membrane integral lipoprotein N-acyltransferase Lnt from P. aeruginosa
ComponentsApolipoprotein N-acyltransferase
KeywordsMEMBRANE PROTEIN / lipoprotein / N-acyltransferase / lipidic cubic phase
Function / homology
Function and homology information


apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / plasma membrane
Similarity search - Function
Apolipoprotein N-acyltransferase / Apolipoprotein N-acyltransferase, N-terminal / Apolipoprotein N-acyltransferase N-terminal domain / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHuang, C.-Y. / Boland, C. / Howe, N. / Wiktor, M. / Vogeley, L. / Weichert, D. / Bailey, J. / Olieric, V. / Wang, M. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Org. Science Foundation IrelandGrant number: 12/IA/1255 Ireland
CitationJournal: Nat Commun / Year: 2017
Title: Structural insights into the mechanism of the membrane integral N-acyltransferase step in bacterial lipoprotein synthesis.
Authors: Wiktor, M. / Weichert, D. / Howe, N. / Huang, C.Y. / Olieric, V. / Boland, C. / Bailey, J. / Vogeley, L. / Stansfeld, P.J. / Buddelmeijer, N. / Wang, M. / Caffrey, M.
History
DepositionFeb 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Experimental preparation / Structure summary
Category: audit_author / exptl_crystal_grow / Item: _audit_author.name / _exptl_crystal_grow.pdbx_details
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 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
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,47910
Polymers58,2301
Non-polymers2,2489
Water28816
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-0 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.730, 39.230, 102.250
Angle α, β, γ (deg.)90.00, 116.26, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Apolipoprotein N-acyltransferase / ALP N-acyltransferase / Copper homeostasis protein CutE homolog


Mass: 58230.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lnt, cutE, PA3984 / Cell line (production host): C41 / Production host: Pseudomonas aeruginosa (bacteria)
References: UniProt: Q9ZI86, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM NaCitrate pH 5.0 30 % (v/v) PEG-500 DME 100 mM sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 3.1→49.5 Å / Num. obs: 10159 / % possible obs: 98.9 % / Redundancy: 5.4 % / Net I/σ(I): 6.48

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
BUSTERrefinement
PHENIX1.10.1_2155refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N6H

5n6h


Resolution: 3.1→49.5 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.84
RfactorNum. reflection% reflection
Rfree0.2729 1005 9.89 %
Rwork0.2247 --
obs0.2295 10157 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 109 16 3918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044009
X-RAY DIFFRACTIONf_angle_d0.8555455
X-RAY DIFFRACTIONf_dihedral_angle_d15.6152282
X-RAY DIFFRACTIONf_chiral_restr0.052594
X-RAY DIFFRACTIONf_plane_restr0.005683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1002-3.26370.46871540.34321296X-RAY DIFFRACTION100
3.2637-3.46810.36321310.2851284X-RAY DIFFRACTION100
3.4681-3.73580.28351520.24131294X-RAY DIFFRACTION100
3.7358-4.11160.28261320.21851310X-RAY DIFFRACTION100
4.1116-4.70610.2521410.20631292X-RAY DIFFRACTION99
4.7061-5.92760.23211470.20861315X-RAY DIFFRACTION99
5.9276-49.50.23831480.20051361X-RAY DIFFRACTION98

+
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