[English] 日本語
Yorodumi
- PDB-4n4r: Structure basis of lipopolysaccharide biogenesis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n4r
TitleStructure basis of lipopolysaccharide biogenesis
Components
  • LPS-assembly lipoprotein LptE
  • LPS-assembly protein LptD
KeywordsMEMBRANE PROTEIN / Beta barrel / Translocase / Lipopolysaccharide transport proteins
Function / homology
Function and homology information


lipopolysaccharide transport => GO:0015920 / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / response to organic substance / lipopolysaccharide binding / cell outer membrane
Similarity search - Function
LptD, C-terminal / LPS-assembly protein LptD / LPS transport system D / Lipoprotein like domain / Lipopolysaccharide-assembly / LPS-assembly lipoprotein LptE / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. ...LptD, C-terminal / LPS-assembly protein LptD / LPS transport system D / Lipoprotein like domain / Lipopolysaccharide-assembly / LPS-assembly lipoprotein LptE / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / Double Stranded RNA Binding Domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / LPS-assembly lipoprotein LptE / LPS-assembly protein LptD
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsDong, H. / Xiang, Q. / Wang, Z. / Paterson, N.G. / He, C. / Zhang, Y. / Wang, W. / Dong, C.
CitationJournal: Nature / Year: 2014
Title: Structural basis for outer membrane lipopolysaccharide insertion.
Authors: Dong, H. / Xiang, Q. / Gu, Y. / Wang, Z. / Paterson, N.G. / Stansfeld, P.J. / He, C. / Zhang, Y. / Wang, W. / Dong, C.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,8168
Polymers225,4124
Non-polymers4054
Water18010
1
A: LPS-assembly protein LptD
B: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9084
Polymers112,7062
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-14 kcal/mol
Surface area32140 Å2
MethodPISA
2
C: LPS-assembly protein LptD
D: LPS-assembly lipoprotein LptE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9084
Polymers112,7062
Non-polymers2022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-11 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.430, 76.082, 213.596
Angle α, β, γ (deg.)90.00, 111.52, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A226 - 786
2010C226 - 786
1020B19 - 169
2020D19 - 169

NCS ensembles :
ID
1
2

-
Components

#1: Protein LPS-assembly protein LptD / Organic solvent tolerance protein


Mass: 90852.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2/ SGSC1412 / ATCC 700720 / Gene: imp, lptD, ostA, STM0093 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q8ZRW0
#2: Protein LPS-assembly lipoprotein LptE


Mass: 21853.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: lptE, rlpB, STM0647 / Plasmid: pACYC-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: Q8ZQZ7
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M zinc acetate, 0.1M sodium cacodylate, 18% PEG8000 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97887, 0.97835, 0.98181, 0.97750
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2013
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978871
20.978351
30.981811
40.97751
ReflectionResolution: 2.8→107.49 Å / Num. obs: 64252 / % possible obs: 9.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.6 / Redundancy: 5.6 % / Rmerge(I) obs: 0.154 / Rsym value: 0.16 / Net I/σ(I): 1.6
Reflection shellResolution: 2.8→3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.904 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.93 / % possible all: 94

-
Processing

Software
NameVersionClassification
EDNAdata collection
SHARPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→107.49 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.907 / SU B: 44.165 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R: 0.667 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.30508 3253 5.1 %RANDOM
Rwork0.28535 ---
obs0.28638 60999 99.83 %-
all-67200 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.272 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å2-0 Å2-0.84 Å2
2--5.33 Å2-0 Å2
3----3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.02 Å0.02 Å
Luzzati d res low-7 Å
Luzzati sigma a0.6 Å0.025 Å
Refinement stepCycle: LAST / Resolution: 2.8→107.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11095 0 12 10 11117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.94315455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49951357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.42824.18610
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.706151712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5831578
X-RAY DIFFRACTIONr_chiral_restr0.1190.21631
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218918
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.448311328
X-RAY DIFFRACTIONr_sphericity_free74.20459
X-RAY DIFFRACTIONr_sphericity_bonded38.785511064
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A7710.1
12C7710.1
21B1810.19
22D1810.19
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 223 -
Rwork0.523 4287 -
obs--99.73 %
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)
11.77520.0523-0.37910.2901-0.44981.7315-0.07140.4820.08670.07490.12330.0245-0.11460.1331-0.05190.7074-0.04410.00440.6519-0.09970.682768.341840.039776.6263
23.77961.3915-2.46960.5562-0.85062.2441-0.2353-0.5614-0.4406-0.2171-0.0046-0.1747-0.28650.17740.23991.29410.2142-0.04650.9484-0.07661.250563.411732.225493.2263
31.4816-0.0303-0.27730.41470.25091.1857-0.0235-0.65110.1468-0.05340.0726-0.03870.0752-0.0217-0.04920.5864-0.11620.00761.0584-0.13330.5771.33655.031727.4759
41.7872-0.4709-1.18710.14580.30190.7985-0.0956-0.2639-0.0145-0.08810.0467-0.0410.1370.12940.04890.7624-0.06850.0230.8688-0.02490.69572.6543-1.74099.5951
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A226 - 786
3X-RAY DIFFRACTION1A801 - 802
4X-RAY DIFFRACTION2B19 - 169
5X-RAY DIFFRACTION3C226 - 786
7X-RAY DIFFRACTION3C801 - 802
8X-RAY DIFFRACTION4D19 - 169

+
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