[English] 日本語
Yorodumi
- PDB-5w8x: Lipid A Disaccharide Synthase (LpxB)-7 solubilizing mutations-Bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w8x
TitleLipid A Disaccharide Synthase (LpxB)-7 solubilizing mutations-Bound to UDP
ComponentsLipid-A-disaccharide synthase
KeywordsTRANSFERASE / glycosyltransferase B / Rossmann-like / C-terminal swap / dimer / lipid A disaccharide synthase / Raetz pathway / lipid A synthesis pathway / lipiopolysaccharide synthesis
Function / homology
Function and homology information


lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / extrinsic component of cytoplasmic side of plasma membrane / extrinsic component of plasma membrane / lipid A biosynthetic process / phospholipid binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Glycosyl transferase, family 19 / Lipid-A-disaccharide synthetase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Lipid-A-disaccharide synthase / Lipid-A-disaccharide synthase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsBohl, T.E. / Aihara, H. / Shi, K. / Lee, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structure of lipid A disaccharide synthase LpxB from Escherichia coli.
Authors: Bohl, T.E. / Shi, K. / Lee, J.K. / Aihara, H.
History
DepositionJun 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipid-A-disaccharide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6862
Polymers42,2821
Non-polymers4041
Water2,198122
1
A: Lipid-A-disaccharide synthase
hetero molecules

A: Lipid-A-disaccharide synthase
hetero molecules


  • defined by author&software
  • Evidence: equilibrium centrifugation, assay for oligomerization, Enzymatic activity assays showed that C-terminal swapped dimer forms and can produce an LpxB mutant heterodimer wherein residues ...Evidence: equilibrium centrifugation, assay for oligomerization, Enzymatic activity assays showed that C-terminal swapped dimer forms and can produce an LpxB mutant heterodimer wherein residues mutated in one subunit are provided in trans by the second subunit to form an intact active site thereby increasing activity. In other words, combining different mutants of LpxB could produce more activity than either mutant alone, which supported the formation of a C-terminally swapped, intact active site.
  • 85.4 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)85,3724
Polymers84,5642
Non-polymers8082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area13700 Å2
ΔGint-124 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.806, 67.806, 153.880
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

DetailsEnzymatic activity assays showed that C-terminal swapped dimer forms and can produce an LpxB mutant heterodimer wherein residues mutated in one subunit are provided in trans by the second subunit to form an intact active site thereby increasing activity. In other words, combining different mutants of LpxB could produce more activity than either mutant alone, which supported the formation of a C-terminally swapped, intact active site.

-
Components

#1: Protein Lipid-A-disaccharide synthase


Mass: 42281.875 Da / Num. of mol.: 1 / Mutation: V66S, V68S, L69S, L72S, L75S, L76S, M207S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: lpxB, ECBD_3437 / Plasmid: pE-SUMO
Details (production host): cleavable His-tagged N-terminal SUMO
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A140NAT1, UniProt: P10441*PLUS, lipid-A-disaccharide synthase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.42 Å3/Da / Density % sol: 49.14 % / Description: bipyramidal
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 39% PEG 4000, 0.6 M LiCl, 0.1 M Tris-HCl pH 8.6 combined 1:1 with 8 g/L protein in 0.3 M NaCl, 5% glycerol, 20 mM Tris-HCl pH 7.4, 5 mM DTT with 100 mM trimethylammonium chloride used as an ...Details: 39% PEG 4000, 0.6 M LiCl, 0.1 M Tris-HCl pH 8.6 combined 1:1 with 8 g/L protein in 0.3 M NaCl, 5% glycerol, 20 mM Tris-HCl pH 7.4, 5 mM DTT with 100 mM trimethylammonium chloride used as an additive at 10 mM or 10% of drop volume

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.98→153.88 Å / Num. obs: 29131 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.035 / Net I/σ(I): 13.2
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.272 / Num. unique obs: 1983 / CC1/2: 0.45 / Rpim(I) all: 0.753 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
PHENIXv1.12_2829refinement
XDSNovember 3, 2014data reduction
Cootv0.8.2model building
PHENIXv1.10_2155phasing
Aimless0.1.27data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.98→54.86 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 24.5
RfactorNum. reflection% reflection
Rfree0.2309 1373 5 %
Rwork0.199 --
obs0.2006 26651 90.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.12 Å2
Refinement stepCycle: LAST / Resolution: 1.98→54.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 25 122 2964
LS refinement shellResolution: 1.98→2.05 Å
RfactorNum. reflection% reflection
Rfree0.3278 102 -
Rwork0.3512 2051 -
obs--75 %
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)
13.50642.1981-0.59723.5726-0.78912.6961-0.28310.4756-0.2797-0.51160.1176-0.24370.53170.32990.20910.3930.0926-0.00260.34620.00530.281-16.147414.2475-47.3201
23.08910.6019-0.39183.3160.11974.52060.02360.01870.1582-0.2666-0.0373-0.2925-0.32590.7033-0.04470.289-0.00140.0470.43450.01510.278413.07337.0764-23.5764
33.1397-0.6815-2.49561.69440.2374.0889-0.2872-0.2529-0.0591-0.05760.1225-0.21930.8460.62670.23430.3650.066-0.01560.35590.00450.29514.951125.394-9.1701
43.58371.08170.5583.7594-0.34234.9019-0.02770.09530.3811-0.1124-0.07710.2611-0.3482-0.3080.11620.2676-0.0040.00210.2806-0.060.329-19.308934.0318-3.585
5-0.4158-0.12691.8172-0.39791.88355.801-0.14410.1810.1336-0.1603-0.06460.06370.25510.34450.12450.563-0.0860.0160.4669-0.02110.3551-11.471420.0427-21.7904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 320 through 381 )A320 - 381
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 139 )A5 - 139
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 185 )A140 - 185
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 275 )A186 - 275
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 319 )A276 - 319

+
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